cromwell — Watchdog Audit

Executive summary

The system holds an adequate standing with an overall health score of 61%, indicating a workable asset that carries significant, concentrated risk. While the codebase is mature and well-structured, its security posture is fragile, creating a vulnerability profile that demands immediate executive attention. The value tied up in this medium-sized system is substantial, requiring approximately 1.3 person-years to rebuild, which translates to a cost of roughly €180,000. This represents a considerable investment in logic and stability that is currently exposed to external threats.

The primary concern is security exposure, which is the system’s weakest lens. With a score of 51%, the application is susceptible to supply-chain attacks and unauthorized code execution. This is not merely a technical debt issue but a direct business risk involving potential data breaches and compliance failures. The lack of strict controls over third-party scripts means that any compromise in an external vendor could directly impact our users and reputation. Addressing this is critical to protecting the asset’s value.

Conversely, the system demonstrates strong internal discipline. The code health and architecture scores are high, reflecting clean, maintainable code that is easy for teams to understand and modify. This structural integrity ensures that when changes are made, they are less likely to introduce defects or ripple effects. The high maturity score further suggests that new team members can onboard quickly, reducing the operational cost of maintenance and future development.

The highest-leverage action is to pin and verify third-party scripts. By specifying exact versions and integrity hashes, or using content security policies for dynamic loaders, we can significantly reduce the attack surface with minimal effort. This step offers the best return on investment by neutralizing the most critical security gaps. Resolving the identified secret leaks in configuration files should follow immediately to prevent credential theft. Focusing on these areas first will stabilize the system’s risk profile without requiring a full rebuild.

Code Health 87% Strong Architecture 85% Adequate · gated by D26 Maturity 65% Adequate · gated by D34 Readiness 65% Adequate · gated by P3 Security 51% Adequate · gated by D29, D36

How the score is built — each lens's share of the headline Width is the lens's weight in the worst-heaviest fold (the weakest area pulls hardest); colour is that lens's own band. A lens fixes the score in proportion to its width.

Security 51% · 47% weightMaturity 65% · 26% weightReadiness 65% · 14% weightArchitecture 85% · 8% weightCode Health 87% · 4% weight

Raise Security 51 → 70 (the Healthy floor) ⇒ headline 61 → ~68.

Code composition — where the lines go

Tests 100%

New since the last scan (2+)

2 finding(s) are new versus the previous scan (2026-09-11) — surfaced by this scheduled scan itself, no pull request required.

D4 · Edited copy of a member (19 corresponding lines) scripts/metadata_comparison/metadata_comparison/lib/operations_digesters.py
D4 · Duplicated block (11 lines × 2) scripts/metadata_comparison/metadata_comparison/lib/operations_digesters.py

A full-fidelity diff against the previous run's complete recorded findings — line-move tolerant: a finding that only shifted line counts as unchanged, only genuinely new titles/files surface here.

Rebuild cost & value ~ Modeled — €61,000–€310,000

Cost to rebuild	€61,000–€310,000 (0.6–1.9 person-years (1,020–3,236 h), ~1–3 engineers)
Domain complexity	Standard — harder problems cost more per line
Quality factor	0.8× (at 61% quality) — the last 20% of quality is most of the work
Size & shape	Medium · effort split not classified (source measured from disk; the effort-tier breakdown is a C#-only syntax walk)

This codebase represents roughly ~1.3 person-years of build effort (about ~€180,000 to rebuild). Its weakest lens is Security at 51% — the part of that asset most exposed by the findings below.

How we model this: boilerplate at a scaffolding rate + logic × domain Standard (×1.0) — standard service × a 0.8× quality factor, at €60–95/h; indicative, ±~30% · size measured directly from source · effort from total production LoC as straight-line logic (the tier split is a C#-only syntax walk), a conservative lower bound. Indicative only — most sensitive to the hourly rate and the domain tier (both tunable in config).

Top priorities

The highest-leverage moves; the full ranked list is in the Roadmap below.

Resolve the 6 REDACTED finding(s) in Secrets (history) — start with REDACTED (6).

+4.9 pts · Low effort · Secrets (history)

Pin third-party scripts and verify them: name an exact version in the URL and add an `integrity="sha384-…"` hash alongside `crossorigin="anonymous"` (both are required — an integrity hash on a cross-origin script without `crossorigin` is not evaluated, it blocks the script). Where the vendor ships a continuously-updated loader and publishes no stable hash (tag managers, analytics, chat widgets), Subresource Integrity is not available: constrain it instead with a `Content-Security-Policy` that names the exact origins allowed to execute, and drop the script from the pages that do not need it. Where the page is shipped inside a package that others host, prefer vendoring the asset and serving it from the app’s own origin, so no consumer inherits a third-party dependency they did not choose.

+9.7 pts · Medium effort · Web-Security Posture

Resolve the 7 REDACTED finding(s) in Static Analysis (SAST) — start with REDACTED (3), REDACTED (2), REDACTED (2).

+3.9 pts · Low effort · Static Analysis (SAST)

Diagnosis — what's actually going on

Value concentrated against a weak lens · Medium · Value at risk

This is a Medium asset (~1.3 person-years to rebuild), and its weakest lens is Security at 51%. The operational and business risk on an asset this size concentrates there — that's where remediation buys the most protection.

Evidence: valuation: Medium, ~1.3 person-years rebuild (96,261 LoC) · weakest lens: Security 51%

→ Direct remediation budget at Security first — highest risk-reduction per euro on an asset this size.

Highest-leverage move · Medium · Leverage

Of everything flagged, the best return on effort is: Pin third-party scripts and verify them: name an exact version in the URL and add an `integrity="sha384-…"` hash alongside `crossorigin="anonymous"` (both are required — an integrity hash on a cross-origin script without `crossorigin` is not evaluated, it blocks the script). Where the vendor ships a continuously-updated loader and publishes no stable hash (tag managers, analytics, chat widgets), Subresource Integrity is not available: constrain it instead with a `Content-Security-Policy` that names the exact origins allowed to execute, and drop the script from the pages that do not need it. Where the page is shipped inside a package that others host, prefer vendoring the asset and serving it from the app’s own origin, so no consumer inherits a third-party dependency they did not choose. The rest can wait behind it.

Evidence: priority ranking: top of 5 ranked by impact/effort

→ Pin third-party scripts and verify them: name an exact version in the URL and add an `integrity="sha384-…"` hash alongside `crossorigin="anonymous"` (both are required — an integrity hash on a cross-origin script without `crossorigin` is not evaluated, it blocks the script). Where the vendor ships a continuously-updated loader and publishes no stable hash (tag managers, analytics, chat widgets), Subresource Integrity is not available: constrain it instead with a `Content-Security-Policy` that names the exact origins allowed to execute, and drop the script from the pages that do not need it. Where the page is shipped inside a package that others host, prefer vendoring the asset and serving it from the app’s own origin, so no consumer inherits a third-party dependency they did not choose.

Architecture — module dependency matrix

Rows and columns are the same modules, ordered so that a module only depends on ones above it. A cell means the row depends on the column, and its number is how many type pairs create that dependency. Read one thing: is anything above the diagonal? A mark there is a dependency cycle. (A cycle is all this shows — an unusual but cycle-free dependency sits below the diagonal like any other.)

536 modules, 1420 dependencies. 16 dependency cycles across 61 modules, marked above the diagonal.

Showing the 40 most-connected modules; 496 more are not drawn.

Module dependency matrix. The row depends on the column; the number is how many type pairs create the dependency. A cell above the diagonal is part of a dependency cycle.
depends on →	2 common.validation	3 cromwell.core.callcaching	4 cromwell.database.sql.tables	5 cromwell.core.path	6 wom.values	7 wdl.model.draft3.elements.ExpressionElement	8 wom.types	9 wdl.draft2.model.expression	10 wom.graph.GraphNodePort	11 wom.expression	12 wom	13 wom.callable	14 wom.graph	15 cromwell.core	16 wdl.draft2.model	17 wom.executable	18 cromwell.core.io	19 cromwell.languages.util	20 cromwell.services.keyvalue.KeyValueServiceActor	21 cromwell.services.metadata	22 cromwell.docker	23 cromwell.languages	24 wdl.model.draft3.elements	25 cromwell.backend	26 wdl.model.draft3.graph	28 cromwell.backend.validation	29 cromwell.engine	31 cromwell.backend.standard	32 cromwell.engine.workflow.lifecycle.execution	34 cromwell.backend.google.batch.models	36 cromwell.engine.workflow.lifecycle.execution.callcaching	38 cromwell.backend.google.batch.util	40 cromwell.backend.google.batch.api
1 common.collections
2 common.validation
3 cromwell.core.callcaching
4 cromwell.database.sql.tables
5 cromwell.core.path														3
6 wom.values	5						12			4
7 wdl.model.draft3.elements.ExpressionElement					1																		85
8 wom.types	2				15
9 wdl.draft2.model.expression					20		3								1
10 wom.graph.GraphNodePort							6						14
11 wom.expression	4				4		2		1
12 wom	1				5					2			1
13 wom.callable	4				3					2	7		6
14 wom.graph	4				1		11		28	6	4	5
15 cromwell.core				2									2
16 wdl.draft2.model	3			1	5		7	3	1	3	4		2
17 wom.executable	4						1			2	1	4	1
18 cromwell.core.io		2		15						1				1
19 cromwell.languages.util	4			1	2				1	3		1		2		1						2
20 cromwell.services.keyvalue.KeyValueServiceActor														1
21 cromwell.services.metadata	4			1	1									4
22 cromwell.docker																	1
23 cromwell.languages	2				1				1	1	1			3		2		1
24 wdl.model.draft3.elements	1					1	1				5	2							2
25 cromwell.backend	1	1		6	9				1	6	1	3	3	11			2		1		1
26 wdl.model.draft3.graph	2						7					2											4
27 wdl.transforms.base.ast2wdlom	14				1	2	1				2	4							3				72
28 cromwell.backend.validation	11				20		4							1										1
29 cromwell.engine		1		4	2						1	1	3	1			2							2
30 wdl.transforms.base.wdlom2wom	8				2		3	9		3	6	5	4			2		2				2	21		6
31 cromwell.backend.standard	1			8	5					1	2	2	8	9			4		2					50		3
32 cromwell.engine.workflow.lifecycle.execution	3			1	3				1				1	16			1							3			3
33 cromwell.engine.workflow.workflowstore			1											18													2
34 cromwell.backend.google.batch.models	3			5	4		2							2							1			2		4		3					1
35 cromwell.backend.impl.aws	4			4	4		4						3	2			3				2			14		5		15
36 cromwell.engine.workflow.lifecycle.execution.callcaching	1	1	2	1										1						1									1
37 cromwell.engine.workflow.lifecycle.execution.job.preparation	3	1			2				1	1			1	1					5		1			2					1
38 cromwell.backend.google.batch.util				2	1												2									6		1		11
39 cromwell.engine.workflow.lifecycle.execution.job		3												3										2					1		1
40 cromwell.backend.google.batch.api														1														1		3		1

Dependency, pointing down the layeringAbove the diagonal — part of a cycleThe module itself

At a glance — Code Health · 87% · Strong ·

The Good

D3 · Scala God Classes 9.5 D4 · Scala Code Duplication 9.7 D17 · Scala Explicit Debt 9.8

The Bad

D1 · Scala Cyclomatic Complexity 6.4 D2 · Scala Cognitive Complexity 5.5

At a glance — Architecture · 85% · Adequate · gated by D26 ·

The Good

D6 · Scala Cohesion (LCOM4) 9.3 D35 · Scala Change Coupling 10.0 AX10 · Repo Code composition 9.6 AX3 · Repo Project dependency cycles 10.0 AX4 · Repo Dependency direction 10.0

The Ugly

D26 · Scala Project Cohesion 0.0

At a glance — Maturity · 65% · Adequate · gated by D34 ·

The Good

D15 · Scala Churn × Complexity Hotspots 10.0 D16 · Scala Bus Factor 9.8 D19 · Scala Documentation Quality 9.0 D21 · Scala Naming Consistency 10.0 M3 · Repo Folder & project structure 10.0 M4 · Repo Documentation accuracy 10.0

The Bad

M2 · Repo Architecture documentation 5.0

The Ugly

D20 · Scala ADR Quality 0.0 D34 · Scala Knowledge Freshness 1.8 M1 · Repo Documentation (README) 4.5

At a glance — Readiness · 65% · Adequate · gated by P3 ·

The Good

D9 · Scala Test Distribution 10.0 D14 · Scala License Compliance 10.0 P1 · Repo CI/CD gates 10.0 P2 · Repo Observability 9.0 P4 · Repo Deployment & Rollback 10.0 P6 · Repo Release Hygiene 10.0 P8 · Repo Schema migrations 10.0

The Bad

D13 · Scala REDACTED Scanning 5.0

The Ugly

P3 · Repo Security & performance tooling 0.0

At a glance — Security · 51% · Adequate · gated by D29, D36 ·

The Good

D31 · Scala IaC & Container Security 7.2 D44 · Scala Platform End-of-Life 10.0

The Bad

S1 · Repo Web-Security Posture 6.0

The Ugly

D28 · Scala Secrets (history) 4.0 D29 · Scala Static Analysis (SAST) 1.1 D36 · Scala Supply-chain Provenance & Signing 0.0

Security & Compliance — OWASP Top-10 mapping

Findings mapped to OWASP categories; the specific CVEs/secrets are in the Security dimension cards below and findings.md (redacted only on the public version of this report).

OWASP category	Findings	Severity
A03:2021 — Injection	44	High / Critical
A05:2021 — Security Misconfiguration	15	High / Critical
A02:2021 — Cryptographic Failures	8	High / Critical

Roadmap

First, harden the web security posture by pinning third-party scripts with integrity hashes and restricting dynamic loaders via Content Security Policy, while vendoring assets where possible. Simultaneously, resolve all identified secrets in the repository history and fix static analysis findings related to hardcoded credentials in CI workflows. Finally, improve onboarding and architectural clarity by adding a quick-start section to the README and documenting key design decisions in a dedicated directory.

Ranked by impact ÷ effort. "Helps" is the estimated gain on the 0–100 health score.

Do this	Helps	Effort	Dimension
Resolve the 6 REDACTED finding(s) in Secrets (history) — start with REDACTED (6).	+4.9 pts	Low	Secrets (history)
Pin third-party scripts and verify them: name an exact version in the URL and add an `integrity="sha384-…"` hash alongside `crossorigin="anonymous"` (both are required — an integrity hash on a cross-origin script without `crossorigin` is not evaluated, it blocks the script). Where the vendor ships a continuously-updated loader and publishes no stable hash (tag managers, analytics, chat widgets), Subresource Integrity is not available: constrain it instead with a `Content-Security-Policy` that names the exact origins allowed to execute, and drop the script from the pages that do not need it. Where the page is shipped inside a package that others host, prefer vendoring the asset and serving it from the app’s own origin, so no consumer inherits a third-party dependency they did not choose.	+9.7 pts	Medium	Web-Security Posture
Resolve the 7 REDACTED finding(s) in Static Analysis (SAST) — start with REDACTED (3), REDACTED (2), REDACTED (2).	+3.9 pts	Low	Static Analysis (SAST)
Resolve the 1 No ADRs found finding(s) in ADR Quality.	+3.7 pts	Low	ADR Quality
Resolve the 1 Leaked secret finding(s) in REDACTED Scanning — start with REDACTED.	+3.1 pts	Low	REDACTED Scanning
Resolve the 3 Most significant orphaned file finding(s) in Knowledge Freshness — start with EngineFunctionEvaluators.scala, WorkflowActor.scala, S3FileSystemProvider.java.	+3.0 pts	Low	Knowledge Freshness
Resolve the 5 REDACTED finding(s) charged to Static Analysis (SAST) — the other 29 are reported here at file:line but scored by D36 (supply-chain provenance), which charges them once.	+2.8 pts	Low	Static Analysis (SAST)
Resolve the 6 High IaC finding(s) in IaC & Container Security — start with REDACTED (3), REDACTED (2), REDACTED.	+1.9 pts	Low	IaC & Container Security

File quality

Per-file score 0–10 — a quality signature. Of 156 files carrying findings, judged against the Production bar: 2% slop · 40% mixed · 58% near-clean.

File	Score	Band	Worst signal
REDACTED	2.1	Slop	IaC & Container Security: High IaC: REDACTED
REDACTED	2.3	Slop	Static Analysis (SAST): High: REDACTED
REDACTED	2.7	Slop	Static Analysis (SAST): High: REDACTED
REDACTED	4.1	Mixed	IaC & Container Security: High IaC: REDACTED
REDACTED	4.4	Mixed	Static Analysis (SAST): High: REDACTED
REDACTED	4.5	Mixed	Static Analysis (SAST): High: REDACTED
REDACTED	4.6	Mixed	Static Analysis (SAST): High: REDACTED
REDACTED	5.1	Mixed	Static Analysis (SAST): High: REDACTED
REDACTED	5.1	Mixed	IaC & Container Security: High IaC: REDACTED
REDACTED	5.8	Mixed	Static Analysis (SAST): High: REDACTED
REDACTED	5.8	Mixed	Static Analysis (SAST): High: REDACTED
wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala	6.0	Mixed	Explicit Debt: TodoComment
backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala	6.0	Mixed	Explicit Debt: TodoComment
engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala	6.0	Mixed	Explicit Debt: FixmeComment
engine/src/main/scala/cromwell/engine/workflow/lifecycle/materialization/MaterializeWorkflowDescriptorActor.scala	6.0	Mixed	Explicit Debt: TodoComment
supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala	6.0	Mixed	Explicit Debt: TodoComment
services/src/main/scala/cromwell/services/cost/GcpCostCatalogService.scala	6.0	Mixed	Explicit Debt: TodoComment
services/src/main/scala/cromwell/services/metadata/impl/archiver/ArchiveMetadataSchedulerActor.scala	6.0	Mixed	Explicit Debt: TodoComment
database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala	6.0	Mixed	Explicit Debt: TodoComment
engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala	6.3	Mixed	God Classes: FileTooLong: job/EngineJobExecutionActor.scala

How the grades work

Every finding carries one of four grades. Three say how serious it is. The fourth says this survey could not settle it — and it is a grade, not a gap.

Critical — 58

A definite problem that already costs you something and drags the score down: a missing authorisation check, a dependency with a known exploit, a build that does not reproduce. Failure here tends to cause failures elsewhere.

Serious — 233

Likely wrong, but not failing yet. It degrades the codebase over a longer horizon and can cause failures elsewhere — not urgent this week, not something to carry for two years either.

Minor — 20

Recorded, with no effect on how the codebase functions. Present so the survey is complete, not because it needs doing.

Could not be resolved — 50

Something this survey could not settle from the outside, and which could be critical or serious. Either a control was required and no positive evidence of it exists in the repository — a backup job that nothing shows was ever restored from proves nothing about restores — or our own analysis could not run over that part of the tree. This is not a clean result. These are excluded from the score rather than awarded a pass, so the number on the cover neither rewards nor penalises them: if you act on this survey without resolving them, you carry that risk yourself. Each one is named under Limitations.

Methodology & how to trust this report

Watchdog is a deep, periodic assessment — run each sprint, monthly, or quarterly, taking the time to go wider and deeper than a quick check and surfacing in one coherent report what you'd otherwise piece together from a dozen separate tools. It scores deterministically: the same commit yields the same score, every run. 32 of 36 evaluated dimensions are computed purely by tools and static analysis (confidence 1.0); 4 documentation/naming judgement(s) are LLM-assisted and labelled advisory. Overall confidence is 0.9 — the weighted average across measured dimensions; it falls as more of the score leans on LLM-assisted judgement and rises when it's fully tool-backed.

Every figure here is one of three kinds, and we label which: ✓ Measured — a deterministic fact (LoC, complexity, coverage); ~ Modeled — an estimate from a stated model (cost, effort, value-at-risk), always a range with its assumptions, never a precise fact; ◐ Advisory — an LLM prose judgement. We never present a modelled estimate as if it were measured. Perfect or absent scores carry their provenance too (ADR-0011): ✓ Tool-verified means the property itself was measured across the surface; ○ Nothing flagged means the probes came back clean — a claim bounded by what a repository can show; ⊘ Not evidenced means a working control (a tested restore, an automated rollback) showed no positive evidence — absence of evidence is not evidence of a control, so it's excluded from the score rather than awarded a spurious 10; ◐ Sampled · advisory marks an LLM verdict over a bounded sample — advisory, never a deterministic measurement.

What we checked — 36 dimensions across the health lenses

D1D2D3D4D6D9D13D14D15D16D17D19D20D21D26D28D29D31D34D35D36D44AX10AX3AX4M1M2M3M4P1P2P3P4P6P8S1

Each chip is a dimension scored from real signals across architecture, testing, dependencies, security & compliance, documentation, git-history and code quality — in one coherent pass. A surface report typically covers a handful.

How to trust any code-health report — three questions

Can you open the finding? Real findings cite a repo-relative file and line you can open at the cited line — never an absolute scratch path. Here, 295 of 311 do; the remainder are repo-wide signals — a dimension-level measurement, not a single line. (Every path in this report is repo-relative by construction: paths are normalized at the producer and the report is rejected if any rooted path leaks through.)
Is there a tool behind the number? Every score below names the method that produced it — Roslyn, git, a scanner, or (for a handful of documentation/naming dimensions) an LLM labelled sampled · advisory — not a narrative.
Does re-running give the same result? Run it again on the same commit and the score — and this report, byte for byte — is identical. A report whose numbers move between runs is describing the run, not the code.

This report answers yes to all three. That's the bar to hold any assessment to.

Tools & methods

The actual versions used this run (captured at analysis time) — re-run on the same commit for the identical score.

Method	Backs	Version	Evaluator
Roslyn static analysis	Complexity, cohesion, coupling, dead code, API surface, layering	5.3.0	✓ deterministic
Native secret scanner	Hardcoded secrets / credentials	1.0.0	✓ deterministic
Watchdog duplication detector (in-process)	Code duplication	1.0.0	✓ deterministic
Coverage (coverlet / dotnet-coverage)	Line & branch coverage	10.0.400	✓ deterministic
NuGet / dotnet	Outdated, vulnerable & deprecated dependencies	10.0.400	✓ deterministic
git / LibGit2Sharp	Churn hotspots, knowledge concentration, history	2.43.0 · 0.31.0	✓ deterministic
gitleaks · semgrep · trivy · checkov	Secrets in history, SAST, CVEs, IaC & container, PII / GDPR	1.86.0 · 0.69.3 · 3.2.533	✓ deterministic
LLM (sampled · advisory)	Documentation quality, ADR conformance, naming — sampled over a bounded sample; advisory, never a deterministic measurement	Local LLM	◐ LLM · sampled · advisory

Every finding is locatable in findings.md. Run 01a0e92f-036f-7d20-b284-eb7320c70831.

The exact command behind every deep-scan dimension — tool, version, invocation and retained raw output — is in Appendix B — Reproduction & audit trail.

Run transparency — what happened this run

What ran differently this time — a tool absent, degraded, or that fell back to an estimate. Named openly, not folded silently into the scores. A degraded run also records its exact cause in diagnostics.md.

D8 Code Coverage — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. Coverage NOT READ here — but this repository measures it: a Codecov configuration (codecov.yml, target 0%) and a coverage step in CI (`codecov/codecov-action`) shows that coverage is collected and tracked in your own CI. The built-in collector has no runner for this ecosystem (.scala, .py), so the analyzer could not read the number — a gap in the analyzer's language coverage, not an unmeasured repo. Not scored. To have the real number read, produce a coverage report in a standard format (`addSbtPlugin("org.scoverage" % "sbt-scoverage" % "<version>")` in `project/plugins.sbt`, then `sbt clean coverage test coverageReport`, or `coverage run -m pytest` then `coverage xml`) and commit it — a hosted scan measures a clone of the repository, so a report that exists only in a working tree, a CI runner's or your own, never reaches it; the artefact is commonly gitignored, so `git add -f` that one file (or un-ignore its path) and commit it alongside the code it measures. You can widen what we reach: optional: produce a coverage report in a standard format (`addSbtPlugin("org.scoverage" % "sbt-scoverage" % "<version>")` in `project/plugins.sbt`, then `sbt clean coverage test coverageReport`, or `coverage run -m pytest` then `coverage xml`) and commit it — a hosted scan measures a clone of the repository, so a report that exists only in a working tree, a CI runner's or your own, never reaches it; the artefact is commonly gitignored, so `git add -f` that one file (or un-ignore its path) and commit it alongside the code it measures — then the real number is read on the next scan.
D11 Test Reliability — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. Test source is present (.scala, .py) and this repository declares an sbt build (repository root, 493 test files), but it was not re-run: the analyzer environment could not run it. Not scored — this is a gap in the analyzer's language coverage, not a finding about this repository.
D12 Dependency Hygiene — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. Dependency Hygiene ran out of its 5-minute budget before it had finished, so what it reports here is a floor rather than a complete count. The rows above are real and stand; what is not known is how many more there are. This is a limit of the analysis run, not a finding about this repository.
D14 License Compliance — measured, with a gap in what it reached — Watchdog measured this, but not all of it. What it did not reach is a gap on our side — a collector, parser or image we have not built yet — so the numbers on that dimension cover less than the repository, and the part left out is not evidence that it would have passed. This repository declares an sbt build (build.sbt), but the licence verdict published here was taken over its JVM dependencies. Nothing was read about its sbt dependencies' licensing in either direction, and a clean score on this card must not be read as covering them.
D22 Internal API Consistency — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. D22 identifies the intentionally-exposed surface from `IsPackable` and `.Contracts` project names, MSBuild conventions read off the loaded project set. This target exposed no such projects, so the probe never ran; this says nothing about whether the repository has a public API. This repository commits no C#/VB source at all, so there was never an MSBuild project set to read these conventions off. That is OUR side and it is a COLLECTOR gap, not an environment fault: no published-package marker D22 reads admitted any project here, so this ecosystem's public API has no collector, and the remedy is to write one — no change to the scan image can close it.
D30 Dependency Vulnerabilities — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. Osv: osv-scanner exited 127 with no findings — dependency CVEs were not measured. 'osv-scanner' exited 127 and produced no findings, and that exit code has no documented repo-side meaning — so this run measured nothing, and nothing here is a statement about the repository.
D43 Malicious Dependencies — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. Osv: osv-scanner exited 127 with no findings — dependency CVEs were not measured. 'osv-scanner' exited 127 and produced no findings, and that exit code has no documented repo-side meaning — so this run measured nothing, and nothing here is a statement about the repository.
AX1 Captive dependencies — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
AX2 Stateful singletons — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
AX6 Interface segregation — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is computed over the public interfaces this run's compilations declare, and none was loaded, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
C1 Data Protection — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. These personal data controls are read from declarative annotations, request middleware, entity/column names and guard methods in a C# source model, and none was loaded on this run, so there was nothing to gather. That is a gap in this analyzer's language reach — not a finding that the repository lacks personal data controls.
C2 Access Controls — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. These authorization controls are read from declarative annotations, request middleware, entity/column names and guard methods in a C# source model, and none was loaded on this run, so there was nothing to gather. That is a gap in this analyzer's language reach — not a finding that the repository lacks authorization controls.
C3 Audit Trail — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. These audit controls are read from declarative annotations, request middleware, entity/column names and guard methods in a C# source model, and none was loaded on this run, so there was nothing to gather. That is a gap in this analyzer's language reach — not a finding that the repository lacks audit controls.
C4 Data Retention — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. These retention controls are read from declarative annotations, request middleware, entity/column names and guard methods in a C# source model, and none was loaded on this run, so there was nothing to gather. That is a gap in this analyzer's language reach — not a finding that the repository lacks retention controls.
C5 Data-Subject Rights — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. These data-subject rights controls are read from declarative annotations, request middleware, entity/column names and guard methods in a C# source model, and none was loaded on this run, so there was nothing to gather. That is a gap in this analyzer's language reach — not a finding that the repository lacks data-subject rights controls.
ED5 Idempotency — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check finds retry-prone mutations by walking the repository's declared types, and NONE was loaded on this run, so it had nothing to look at. That is a limit of the analyzer's reach — it reads .NET projects — not a finding that this repository has no command handlers or message consumers.
GD1 Unfinished & placeholder code — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
IC1 Incompleteness & stubs — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
P10 Library API & versioning — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check reads NuGet packaging and C# public API only, and no .NET project was loaded for this repository, so it had nothing of this repository's product to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
PF1 Benchmark discipline — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
PF2 Allocation hygiene — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
PF3 Async & latency hygiene — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. Those languages colour their functions async, so blocking inside them is the same defect this card counts elsewhere, but their blocking vocabulary is not modelled yet. That is a gap in this analyzer's language reach — not a finding that the code is free of it.
X1 Async correctness — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X10 Duplicated predicate — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X12 Unreachable branch — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X13 Undrained process stream — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X14 Bypassable address classification — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X15 Unvalidated length from an untrusted reader — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X16 Unfloored truncation loop — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X17 Uncapped recursion over a caller-supplied document — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X18 Disposal-pattern correctness — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X19 Unrestored process-global state — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X2 Cancellation propagation — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X20 Mistyped argument guard — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X21 Side-effecting pattern guard — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X22 Contradicted release guard — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X23 Unguarded diagnostic materialisation — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X24 Document value interpolated into markup unescaped — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X25 Inert configuration knob — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X26 Unsynchronised callback handoff — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X27 Collection changed while being enumerated — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X28 Index access outside its own emptiness guard — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X29 Per-element action decided by a fixed element — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X3 Exception handling — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X30 Support guard that admits what it rejects — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X32 Type resolved by simple name across every loaded assembly — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X4 Structured logging — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X5 Nullable reference types — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X6 Hand-rolled structured-format parsing — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X7 Silent fallback defaults — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.

Repo exclusion declarations (.gitattributes linguist-generated/vendored, .editorconfig generated_code): none declared — every source file was scored.

Limitations & what we did not check

Watchdog assesses the repository exactly as committed, and only the repository. By design it does not reach outside the source tree: the live cloud account, the running CI/CD pipeline, the host's branch-protection and approval rules, the production configuration, or a restore actually exercised against a backup are all out of scope. That boundary is a feature, not a gap — a repo-relative, deterministic scan re-runs identically on any commit and every finding opens at a real file and line, where a live audit can neither be reproduced nor traced. The visible consequence is that controls which leave no in-repo evidence are reported as "not evidenced" and excluded from the score rather than awarded a number a static scan cannot justify.

Per-dimension blind spots

For each dimension that was measured, what a static, repo-only scan structurally cannot see — the honest edge of the measurement, not a failure of it.

D1 Cyclomatic Complexity: Cyclomatic complexity counts branches statically — it cannot tell an essential decision tree from accidental tangle, nor see complexity that lives in data or configuration (large switch-case token tables, DSL lexers/parsers, data-as-code rule tables) rather than control flow: a tokenizer's many single-character cases read as high complexity though each branch is trivial.
D2 Cognitive Complexity: Cognitive-complexity heuristics approximate how hard code is to follow; genuine domain difficulty and well-named intent that eases reading are not captured.
D3 God Classes: "God class" is sized by members and responsibilities visible in the type — a deliberately broad facade over a coherent subsystem can read the same as an accidental grab-bag. For front-end JS the file-length check is cohesion-aware (a single-responsibility module — one class/IIFE — earns a 3× threshold), but cohesion is approximated from top-level declarations, not true dependency structure.
D4 Code Duplication: Duplication is token-similarity — an in-process token-stream comparison over sliding windows, with type-aware normalization — so it finds copy-paste, not semantic duplication expressed differently. Committed machine-written code (scaffolded migrations, designer/codegen output, protobuf/OpenAPI stubs, model snapshots) is EXCLUDED — its repetition is the tool's, not the team's — so the score reflects hand-written duplication only.
D6 Cohesion (LCOM4): LCOM4 cohesion is syntactic — it infers connectivity from which methods touch which fields/methods by name, not from real runtime behaviour or intent.
D9 Test Distribution: The test-pyramid shape is inferred from project/folder naming and references, with a single test host bucketed per-file by its path tier and content signals — a suite that names tiers unconventionally and gives no per-file signal can still be mis-bucketed.
D13 REDACTED Scanning: REDACTED detection is signature- and entropy-based on the current tree — a secret that does not match a known pattern, or one already rotated, will not be flagged (a clean scan is "nothing matched", not "no secrets exist").
D14 License Compliance: License compatibility is checked against declared package metadata and a policy — mislabelled or missing license metadata, and obligations that depend on how you distribute, are not resolved here.
D15 Churn × Complexity Hotspots: Churn hotspots come from git history — a freshly imported or squashed repository has no churn signal, and recent rewrites can mask a historically risky file.
D16 Bus Factor: Bus-factor is a time-decayed model of commit attribution (who has recently, repeatedly worked a file), not comprehension — pairing, review and reading-without-committing spread knowledge it can't see; bot commits and shared accounts still distort it.
D17 Explicit Debt: Acknowledged-debt signals (TODO/FIXME, suppressions, dead code) are textual — undocumented debt that nobody marked, and debt that lives in design rather than annotations, is invisible. Committed machine-written code (scaffolded migrations, designer/codegen output, generated stubs) is excluded — it is never the team's dead code to delete.
D19 Documentation Quality: Documentation quality is judged by an LLM over a bounded sample of docs — it reads what is written, not whether the docs match the running system, and it is advisory, not a measurement. Its critique rows are drawn from a closed category vocabulary and each row means the same thing in every run, so two scans can be compared row by row; the SET that fires is still a sample, and does not repeat exactly. Measured on one frozen input, six scans at one engine SHA: 2-5 critique rows per scan, 8 distinct rows across the six, 3 of those 8 seen in only one scan. So a D19 row is evidence about the documentation, but a COUNT of D19 rows is not a quantity — never read a change in it as an improvement or a regression.
D20 ADR Quality: ADR quality is an LLM read of the decision records present — it cannot know about decisions made and never recorded, and its verdict is sampled and advisory.
D21 Naming Consistency: Naming quality is an LLM judgement over a bounded sample — it assesses clarity/consistency of the names it sees, not domain-correctness, and is advisory.
D26 Project Cohesion: Project focus is sized from members/namespaces per project — a project that is broad by deliberate design reads the same as one that has sprawled.
D28 Secrets (history): Secret-history scanning sweeps the git log for known patterns — a secret that predates the available history, or never matched a signature, is not found (clean means "nothing matched in the history we can see").
D29 Static Analysis (SAST): SAST findings are pattern-based (semgrep) — it finds classes of bug it has rules for; logic flaws, auth/authorization gaps and issues needing runtime context are out of reach (and clean means "no rule matched").
D31 IaC & Container Security: IaC scanning checks Dockerfiles/Terraform/Kubernetes against best-practice rules — it cannot see the live cloud account, runtime configuration, or drift between the committed config and what is actually deployed.
D34 Knowledge Freshness: Freshness is decayed commit RECENCY, not comprehension — code read often but rarely committed reads as orphaned, and stable code that genuinely needs no changes is penalised the same as forgotten code; bot/squash commits distort it like the bus factor.
D35 Change Coupling: Change coupling is co-change in COMMITS — files split across separate commits, or coupled only through a shared config/build step, read as uncoupled, and a sweeping commit (rename/format) is excluded so it doesn't couple everything. It shows that files change together, not WHY: a high coupling can be a healthy cohesive pair as readily as a hidden leak.
D44 Platform End-of-Life: The support table is FROZEN, so it goes out of date by losing RECALL: a release that ended support after the table was written is missed until the table is refreshed, and this dimension reading 10 is not evidence that a platform is current. Only platforms the repository DECLARES in a place this pass reads are seen — a runtime named only in a REDACTED (D31's subject), in a CI workflow (D29's), or in a file this pass does not parse (go.mod, a Gemfile ruby directive) is invisible here, which is why a repository declaring none of them abstains rather than scoring. Only frameworks with a PUBLISHED support policy are tracked: React, Flask and Express publish none, so their age cannot be judged and their absence from a report is not a statement that they are supported.
AX10 Code composition: Role is inferred from namespace/folder convention, not semantics — a domain concept living in a folder named "Services" reads as application, and the split is lines-of-code, not business value. The business-logic-share score is a SOFT, FLOORED signal: it contributes to the Architecture lens but is floored at the Critical gate, so an infrastructure-heavy design (a gateway, an ETL, a driver) is legitimately low without being nuked to zero.
M4 Documentation accuracy: Onboarding quality is an LLM read of the docs/setup present — it cannot run the onboarding or measure how long a real new joiner takes; the verdict is sampled and advisory.
P4 Deployment & Rollback: Approval/branch-protection rules live in repository settings the scan cannot see — only their in-repo evidence (config files, workflows) is checked, so a control enforced purely in the host's settings reads as "not evidenced".
P6 Release Hygiene: Rollback/observability controls are inferred from repo artefacts (pipelines, dashboards-as-code) — controls configured in external tooling, with no in-repo trace, cannot be credited.

The LLM boundary

LLM-set scores this run (4): D19, D21, D26, M4 (model: Local LLM). For these, a model reads a bounded sample and sets the numeric score; each names its own sample and method on its card. They are sampled and advisory by design: they vary at the margins between runs and are never a deterministic measurement. Every other score in this report is tool-computed at confidence 1.0.

Dimensions

D1 · Cyclomatic Complexity6.4 / 10Adequate✓ Tool-verified

What it measures: How tangled the control flow is — methods with many branches are hard to test and change.

Method: Cyclomatic complexity per method (1 + decision points), computed exhaustively across production source; test projects separated by convention. Deterministic.

Maturity: Documented → Verified → Prevented · effective 6.4 / 10 · rule-coverage 100% · ceiling Prevented

22 method(s) exceeded the cyclomatic complexity threshold of 15; the worst was ValueEvaluator.evaluate at 85. A further 1 method(s) were over the threshold but excluded as flat dispatchers (a long switch/match over independent cases: many branches, almost no nesting), the largest being WdlExpression.toString at 29 — they are counted neither in the figure above nor in this dimension's score. 1 file carries no cyclomatic complexity row at all for this reason — every one of its over-threshold methods was excluded, so the exclusion is disclosed nowhere in the file itself: wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlExpression.scala (WdlExpression.toString at 29). They are named here because the per-file figures other dimensions report are taken BEFORE this exclusion, so such a file can show a high maximum complexity elsewhere in this report and nothing here, with nothing to reconcile the two.

ValueEvaluator.evaluate (cyclomatic 85)wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/ValueEvaluator.scala:51

TypeEvaluator.evaluate (cyclomatic 84)wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala:20

WdlNamespace.apply (cyclomatic 54)wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlNamespace.scala:198

CallElementToGraphNode.convert (cyclomatic 36)wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/CallElementToGraphNode.scala:31

FileEvaluator.evaluateRecursive (cyclomatic 35)wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/FileEvaluator.scala:71

+ 17 more group(s) — more in Appendix A; the complete list is findings.md.

What to do

Resolve the 1 ValueEvaluator.evaluate (cyclomatic 85) finding(s) in Cyclomatic Complexity — start with ValueEvaluator.scala. — One of this dimension's main actionable groups (1 warning-level).
Resolve the 1 TypeEvaluator.evaluate (cyclomatic 84) finding(s) in Cyclomatic Complexity — start with TypeEvaluator.scala. — One of this dimension's main actionable groups (1 warning-level).
Resolve the 1 WdlNamespace.apply (cyclomatic 54) finding(s) in Cyclomatic Complexity — start with WdlNamespace.scala. — One of this dimension's main actionable groups (1 warning-level).
Enforce Cyclomatic Complexity in CI to reach Verified (currently Documented). — Hardens enforcement from Documented toward Prevented — provenance only; does not change the score.

Detailed fixes: d1_recommendation.md · top locations in Appendix A, every location in findings.md.

Do you agree with this assessment?

D2 · Cognitive Complexity5.5 / 10Adequate✓ Tool-verified

What it measures: How hard the code is for a person to follow, beyond raw branching.

Method: Cognitive complexity per method (Sonar-style nesting-penalized score), computed exhaustively over production code, excluding test projects. Deterministic.

Maturity: Documented → Verified → Prevented · effective 5.5 / 10 · rule-coverage 100% · ceiling Prevented

31 method(s) exceeded the cognitive complexity threshold of 15; the worst was ValueEvaluator.evaluate at 157.

ValueEvaluator.evaluate (cognitive 157)wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/ValueEvaluator.scala:51

TypeEvaluator.evaluate (cognitive 147)wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala:20

FileEvaluator.evaluateRecursive (cognitive 79)wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/FileEvaluator.scala:71

WdlNamespace.apply (cognitive 61)wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlNamespace.scala:198

MaterializeWorkflowDescriptorActor.buildWorkflowDescriptor (cognitive 53)engine/src/main/scala/cromwell/engine/workflow/lifecycle/materialization/MaterializeWorkflowDescriptorActor.scala:304

+ 26 more group(s) — more in Appendix A; the complete list is findings.md.

What to do

Resolve the 1 ValueEvaluator.evaluate (cognitive 157) finding(s) in Cognitive Complexity — start with ValueEvaluator.scala. — One of this dimension's main actionable groups (1 warning-level).
Resolve the 1 TypeEvaluator.evaluate (cognitive 147) finding(s) in Cognitive Complexity — start with TypeEvaluator.scala. — One of this dimension's main actionable groups (1 warning-level).
Resolve the 1 FileEvaluator.evaluateRecursive (cognitive 79) finding(s) in Cognitive Complexity — start with FileEvaluator.scala. — One of this dimension's main actionable groups (1 warning-level).
Enforce Cognitive Complexity in CI to reach Verified (currently Documented). — Hardens enforcement from Documented toward Prevented — provenance only; does not change the score.

Detailed fixes: d2_recommendation.md · top locations in Appendix A, every location in findings.md.

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D3 · God Classes9.5 / 10Stronggated by 13 serious findings✓ Tool-verified

What it measures: Over-large classes that try to do too much ("god classes").

Method: God-class detection by line and method-count thresholds per logical type (partial classes unified), filtered for generated code and registration/contract false positives. Deterministic.

Maturity: Documented → Verified → Prevented · effective 9.5 / 10 · rule-coverage 100% · ceiling Prevented

13 god class(es) detected.

FileTooLong: actors/GcpBatchAsyncBackendJobExecutionActor.scala · ×7supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala

TooManyMethods: BetterFileMethods · ×6core/src/main/scala/cromwell/core/path/BetterFileMethods.scala:25

What to do

Resolve the 7 FileTooLong finding(s) in God Classes — start with GcpBatchAsyncBackendJobExecutionActor.scala, EngineJobExecutionActor.scala, StandardAsyncExecutionActor.scala. — One of this dimension's main actionable groups (7 warning-level).
Resolve the 6 TooManyMethods finding(s) in God Classes — start with WdlStandardLibraryFunctions.scala (2), BetterFileMethods.scala, StandardAsyncExecutionActor.scala. — One of this dimension's main actionable groups (6 warning-level).
Enforce God Classes in CI to reach Verified (currently Documented). — Hardens enforcement from Documented toward Prevented — provenance only; does not change the score.

Detailed fixes: d3_recommendation.md · top locations in Appendix A, every location in findings.md.

Do you agree with this assessment?

D4 · Code Duplication9.7 / 10Stronggated by 58 serious findings✓ Tool-verified

What it measures: Copy-pasted code that should be shared instead.

Method: Code duplication via token-stream sliding windows with type-aware normalization (locals masked, type names preserved), density-scored per KLoC of production code. Deterministic.

Maturity: Documented → Verified → Prevented · effective 9.7 / 10 · rule-coverage 100% · ceiling Verified

54 duplicated block group(s) detected. A further 4 rows report members as variants of one another; they aggregate block groups already counted above and are not themselves counted.

Duplicated block (6 lines × 2) · ×6wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/FileEvaluator.scala:163

Duplicated block (5 lines × 2) · ×6database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala:260

Duplicated block (11 lines × 2) · ×5backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala:1111

Duplicated block (7 lines × 2) · ×5cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/GoogleConfiguration.scala:107

Duplicated block (8 lines × 2) · ×4engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala:225

+ 27 more group(s) — more in Appendix A; the complete list is findings.md.

What to do

Resolve the 6 Duplicated block (6 lines × 2) finding(s) in Code Duplication — start with TypeEvaluator.scala (2), FileEvaluator.scala, BiscayneValueEvaluators.scala. — One of this dimension's main actionable groups (6 warning-level).
Resolve the 6 Duplicated block (5 lines × 2) finding(s) in Code Duplication — start with GcpBatchRuntimeAttributes.scala (2), MetadataEntryComponent.scala, TypeEvaluator.scala. — One of this dimension's main actionable groups (6 warning-level).
Resolve the 5 Duplicated block (11 lines × 2) finding(s) in Code Duplication — start with StandardAsyncExecutionActor.scala, RuntimeAttributesValidation.scala, TaskDefinitionElementToWomTaskDefinition.scala. — One of this dimension's main actionable groups (5 warning-level).
Enforce Code Duplication in CI to reach Verified (currently Documented). — Hardens enforcement from Documented toward Verified — provenance only; does not change the score.

Detailed fixes: d4_recommendation.md · top locations in Appendix A, every location in findings.md.

Do you agree with this assessment?

D6 · Cohesion (LCOM4)9.3 / 10Stronggated by 6 serious findings✓ Tool-verified

What it measures: Whether a class's methods are focused on a single responsibility.

Method: LCOM4 cohesion per production class with at least two methods: connected components of methods sharing state or calls, computed syntactically. Deterministic, not a proxy.

Coverage: Exhaustive · type-level: LCOM4 cohesion computed over every production class — the population is all types, not a name convention.

Maturity: Documented → Verified → Prevented · effective 9.3 / 10 · rule-coverage 100% · ceiling Verified

6 of 105 classes have LCOM4 above 3.

Low cohesion: TesAsyncBackendJobExecutionActor (LCOM4 7) · ×6supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala:222

What to do

Resolve the 6 Low cohesion finding(s) in Cohesion (LCOM4) — start with TesAsyncBackendJobExecutionActor.scala, WorkflowDockerLookupActor.scala, SubWorkflowExecutionActor.scala. — One of this dimension's main actionable groups (6 warning-level).
Enforce Cohesion (LCOM4) in CI to reach Verified (currently Documented). — Hardens enforcement from Documented toward Verified — provenance only; does not change the score.

Detailed fixes: d6_recommendation.md · top locations in Appendix A, every location in findings.md.

Do you agree with this assessment?

D9 · Test Distribution10.0 / 10Exemplary✓ Tool-verified

What it measures: Whether the test suite has a healthy mix of unit / integration / end-to-end tests.

Method: Test projects classified (Unit/Integration/BDD/E2E) from compiled metadata; test methods counted exhaustively across projects with placement-agnostic disk fallback. Deterministic.

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Documented

29 test methods: 29 unit, 0 integration, 0 BDD, 0 e2e. The Python suite contributes 24 test function(s) across 8 file(s) declaring at least one — every `def test…` in a file pytest or unittest would collect, which is those frameworks' own definition of a case; a parametrize table counts once, so this is a floor. Its tier split is read from file names and paths only.

✓ On the Gold path — maintain.

Detailed fixes: d9_recommendation.md.

Do you agree with this assessment?

D13 · REDACTED Scanning5.0 / 10Adequate✓ Tool-verified

What it measures: Whether any secrets (keys, tokens, passwords) have leaked into the code.

Method: In-process native secret scanner (entropy plus signature patterns) across all tracked files; no external tool. A clean result is a measured 10, not no-data zero. Deterministic.

Maturity: Documented → Verified → Prevented · effective 5.0 / 10 · rule-coverage 100% · ceiling Prevented

1 secret(s) detected.

REDACTED

What to do

Resolve the 1 Leaked secret finding(s) in REDACTED Scanning — start with REDACTED. — One of this dimension's main actionable groups (1 issue-level).
Enforce REDACTED Scanning in CI to reach Verified (currently Documented). — Hardens enforcement from Documented toward Prevented — provenance only; does not change the score.

Detailed fixes: d13_recommendation.md · top locations in Appendix A, every location in findings.md.

Do you agree with this assessment?

D14 · License Compliance10.0 / 10Exemplary○ Nothing flagged

What it measures: Whether the licenses of third-party packages are compatible with your policy.

Method: Third-party package licenses resolved from declared package metadata and checked against the configured policy (allow/deny/copyleft). Deterministic; clean = no incompatible license found at metadata depth.

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Verified

0 of 5 declared JVM dependency artifact(s) use a banned license. Licences were resolved from the POMs Maven Central publishes, over the coordinates this repository's 1 Maven/Gradle manifest(s) declare with a version resolvable from the manifest itself — the same declaration-site closure this analysis reads for dependency currency. The JVM has no lockfile a checkout is guaranteed to carry, so this is deliberately NOT the transitive closure. ★ COVERAGE OF THIS VERDICT: it grades this repository's JVM dependencies and nothing else. The repository also declares an sbt build (build.sbt), and the licences of those dependencies were NOT read by this pass — a gap in this engine's coverage, not a statement about them. So this result says the graded closure carries no banned licence; it does NOT say this repository's licensing is clear.

✓ On the Gold path — maintain.

Detailed fixes: d14_recommendation.md.

Do you agree with this assessment?

D15 · Churn × Complexity Hotspots10.0 / 10Exemplary✓ Tool-verified

What it measures: Files that change often and are also complex — the riskiest hotspots.

Method: Per production file churn times cyclomatic complexity over a rolling window, computed from git and Roslyn/JS/Razor analysis. Exhaustive, deterministic per commit date.

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Documented

No churn × complexity hotspots in the window.

✓ On the Gold path — maintain.

Detailed fixes: d15_recommendation.md.

Do you agree with this assessment?

D16 · Bus Factor9.8 / 10Exemplary✓ Tool-verified

What it measures: Whether knowledge is concentrated in too few people (the "bus factor").

Method: Living knowledge per author via time-decayed commit attribution (6-month half-life, focus weighting) across largest source files. Deterministic, avoids blame's mechanical-refactor false positives.

Maturity: Documented → Verified → Prevented · effective 9.8 / 10 · rule-coverage 100% · ceiling Documented

10 source file(s) have their living knowledge concentrated in one author (≥90% of recent, decayed contribution). The largest is engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ExecutionStore.scala. Counted over 489 of the 1152 production source files in this repository: 652 are under the ~2,400-byte size floor this dimension measures over, and the remaining 11 have no attributable history left to measure.

Off-boarding risk: anonymized user #1

Further sole-owners (lower concentration)

✓ On the Gold path — maintain.

Detailed fixes: d16_recommendation.md · top locations in Appendix A, every location in findings.md.

Do you agree with this assessment?

D17 · Explicit Debt9.8 / 10Stronggated by 87 serious findings✓ Tool-verified

What it measures: Acknowledged debt left in the code — TODOs, dead code, suppressed warnings.

Method: Roslyn syntactic debt markers (suppressions/TODO/FIXME/HACK/empty-catch/commented-code/Obsolete) plus SymbolFinder dead-code analysis; weighted-debt-per-KLoC density deducted 2.0x per unit. Deterministic, exhaustive.

Maturity: Documented → Verified → Prevented · effective 9.8 / 10 · rule-coverage 100% · ceiling Prevented

87 deducted task-comment markers across 96261 LoC (0.1/KLoC) → score 9.8. Task comments only: this repository's language is read without a compiler, so D17's suppression, dead-code and commented-out-code arms did not run and this score counts fewer marker kinds than a .NET repository's would.

TodoComment · ×78CromIAM/src/test/scala/cromiam/webservice/SwaggerUiHttpServiceSpec.scala:47

FixmeComment · ×9CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala:31

What to do

Resolve the 78 TodoComment finding(s) in Explicit Debt — start with MetadataEntryComponent.scala (4), TesTask.scala (4), MaterializeWorkflowDescriptorActor.scala (3). — One of this dimension's main actionable groups (78 warning-level).
Resolve the 9 FixmeComment finding(s) in Explicit Debt — start with SubmissionSupport.scala (3), WesRouteSupport.scala (2), CromIamApiService.scala. — One of this dimension's main actionable groups (9 warning-level).
Enforce Explicit Debt in CI to reach Verified (currently Documented). — Hardens enforcement from Documented toward Prevented — provenance only; does not change the score.

Detailed fixes: d17_recommendation.md · top locations in Appendix A, every location in findings.md.

Do you agree with this assessment?

D19 · Documentation QualityExemplary◐ Sampled · advisory

What it measures: Whether the project's documentation is clear, complete, and useful.

Method: Judged by language model at low temperature (0.0-0.1) on a deterministic doc sample (READMEs plus first 25 architecture docs), with two-pass stability filtering. Advisory, sampled.

Maturity: Documented → Verified → Prevented · effective Exemplary / 10 · rule-coverage 100% · ceiling Documented

The repository's root README and a dedicated Cromwell documentation site (readthedocs.io) give an excellent overview of what Cromwell is, its licensing, tutorials, the contributor guide, ecosystem, and roadmap. The architecture/Docs markdown files provide comprehensive architecture and design documentation for each backend provider type (cloud providers, containers, workflow managers), with detailed provider examples and a full backends list. A focused README for each directory documents that directory rather than the repository as a whole, so any missing installation or usage guidance is confined to the root level. Cromwell's documentation is comprehensive and well-structured: a README for each directory (GettingHelp, Imports, LanguageSupport, Logging, Modes, Releases, RuntimeAttributes, Scaling, WOMtool) gives the purpose of its own tier plus installation/usage guidance. The architecture/design docs are separate and fully referenced; there is no single root README covering overview, installation, usage, contribution, or license. All visible documents are complete with headings (e.g., 'Recognized Runtime attributes and Backends') and the outline sections present.

Documentation: no licence statementdocs/index.md

✓ On the Gold path — maintain.

Detailed fixes: d19_recommendation.md · top locations in Appendix A, every location in findings.md.

Do you agree with this assessment?

D20 · ADR Quality0.0 / 10Critical✓ Tool-verified

What it measures: Whether architecture decisions are recorded well (context, decision, consequences).

Method: Per-ADR judgment by language model at low temperature with two-pass stability; confidence is share of ADRs evaluated; enforcement-field presence detected deterministically. Advisory.

Maturity: Documented → Verified → Prevented · effective 0.0 / 10 · rule-coverage 100% · ceiling Documented

No architecture decision records were found.

No ADRs found

What to do

Resolve the 1 No ADRs found finding(s) in ADR Quality. — One of this dimension's main actionable groups (1 recommendation-level).

Detailed fixes: d20_recommendation.md · top locations in Appendix A, every location in findings.md.

Do you agree with this assessment?

D21 · Naming ConsistencyExemplary◐ Sampled · advisory

What it measures: Whether names — types, methods, variables — are clear and consistent.

Method: Judged by language model at low temperature (0.0-0.1) on a deterministic random symbol sample (fixed size, not exhaustive), with disclosed confidence band. Advisory, sampled.

Maturity: Documented → Verified → Prevented · effective Exemplary / 10 · rule-coverage 100% · ceiling Verified

0 naming inconsistencies across 0 sampled symbols.

✓ On the Gold path — maintain.

Detailed fixes: d21_recommendation.md.

Do you agree with this assessment?

D26 · Project Cohesion0.0 / 10Critical✓ Tool-verified

What it measures: Whether each project is a focused, coherent unit rather than an oversized grab-bag.

Method: Project size overshoot penalties (LoC / public-type count / namespace count, 2-of-3 flag) weighted by log magnitude. Exhaustive across projects, deterministic, LLM-independent.

Maturity: Documented → Verified → Prevented · effective 0.0 / 10 · rule-coverage 100% · ceiling Documented

1 of 2 build units (sbt) flagged as possibly oversized/incoherent.

Projects may be oversized for their cohesion

What to do

Resolve the 1 Projects may be oversized for their cohesion finding(s) in Project Cohesion. — One of this dimension's main actionable groups (1 recommendation-level).

Detailed fixes: d26_recommendation.md · top locations in Appendix A, every location in findings.md.

Do you agree with this assessment?

D28 · Secrets (history)4.0 / 10Weak✓ Tool-verified

What it measures: Whether any secrets were ever committed — scanned across the full git history, not just now.

Method: REDACTED scan via TWO gitleaks detect passes in an isolated checkout — the full git history, then a second --no-git pass over the working tree as it stands — merged and de-duplicated by (rule, file, line); each match flagged High. Both invocations are recorded in the audit trail. Exhaustive; when the tool is absent, or when its output cannot be parsed into the expected shape, the dimension is WITHHELD as an explicit measurement gap on our side — unscored and excluded from the lens, never a hedged middling score.

Maturity: Documented → Verified → Prevented · effective 4.0 / 10 · rule-coverage 100% · ceiling Documented

6 finding(s): 0 critical, 6 high, 0 medium, 0 low. Remediation for historically-committed secrets is credential rotation — they remain in history regardless of later deletion.

REDACTED

What to do

Resolve the 6 REDACTED finding(s) in Secrets (history) — start with REDACTED (6). — One of this dimension's main actionable groups (6 issue-level).
Resolve the 1 Rotate the exposed credentials finding(s) in Secrets (history). — One of this dimension's main actionable groups (1 recommendation-level).

Detailed fixes: d28_recommendation.md · top locations in Appendix A, every location in findings.md.

Do you agree with this assessment?

D29 · Static Analysis (SAST)1.1 / 10Critical✓ Tool-verified

What it measures: Real static-analysis (SAST) findings — likely security bugs in the code, any language.

Method: Polyglot static analysis via semgrep across the repo using the pinned, image-baked p/security-audit + p/owasp-top-ten rulesets (no scan-time registry fetch); severity rules (ERROR/WARNING/INFO) map to a full-band severity-weighted score. Exhaustive, deterministic; degrades on parse failure.

Coverage: semgrep pattern rules over all files — exhaustive for the rule set, blind to classes of bug without a rule (clean = no rule matched).

Maturity: Documented → Verified → Prevented · effective 1.1 / 10 · rule-coverage 100% · ceiling Documented

44 finding(s): 0 critical, 41 high, 2 medium, 1 low. 29 unpinned-GitHub-Actions row(s) are reported here but scored by D36 (supply-chain provenance), which measures that posture as `pinned_actions` — one pinning decision is charged once, not once per lens. semgrep hit a parse error in 3 file(s) — `scripts/reference_disks/create_images.sh` (lines 100–390), `src/ci/bin/test-deadlock.sh` (line 56), `src/ci/bin/test_slurm.inc.sh` (line 55) — so no absence of findings in the named regions is evidence of anything; rows reported elsewhere in those files are real. Fix the syntax error (or exclude the file deliberately) and re-scan to cover them. Separately, one or more rules could not re-parse an embedded snippet in 1 file(s) (e.g. a workflow `run:` block read as shell). Those files WERE scanned and their other rows are unaffected; only those rules' view of those snippets is missing.

REDACTED

What to do

Resolve the 7 REDACTED finding(s) in Static Analysis (SAST) — start with REDACTED (3), REDACTED (2), REDACTED (2). — One of this dimension's main actionable groups (7 issue-level).
Resolve the 5 REDACTED finding(s) charged to Static Analysis (SAST) — the other 29 are reported here at file:line but scored by D36 (supply-chain provenance), which charges them once. — One of this dimension's main actionable groups (34 issue-level, 5 of them charged here).
Resolve the 2 REDACTED finding(s) in Static Analysis (SAST) — start with REDACTED, REDACTED. — One of this dimension's main actionable groups (2 warning-level).

Detailed fixes: d29_recommendation.md · top locations in Appendix A, every location in findings.md.

Do you agree with this assessment?

D31 · IaC & Container Security7.2 / 10Adequategated by 6 critical findings✓ Tool-verified

What it measures: Whether Dockerfiles / Terraform / Kubernetes config follow security best practices.

Method: IaC/container misconfiguration scan via trivy config (REDACTED/Terraform/K8s/Helm/CloudFormation); severity rules to 0-10 moderate normalizer. NotApplicable without manifests. Exhaustive, deterministic.

Maturity: Documented → Verified → Prevented · effective 7.2 / 10 · rule-coverage 100% · ceiling Documented

15 finding(s): 0 critical, 6 high, 7 medium, 2 low.

REDACTED

What to do

Resolve the 6 High IaC finding(s) in IaC & Container Security — start with REDACTED (3), REDACTED (2), REDACTED. — One of this dimension's main actionable groups (6 issue-level).
Resolve the 7 Medium IaC finding(s) in IaC & Container Security — start with REDACTED (3), REDACTED (3), REDACTED. — One of this dimension's main actionable groups (7 warning-level).
Resolve the 2 Low IaC finding(s) in IaC & Container Security — start with REDACTED (2). — One of this dimension's main actionable groups (2 recommendation-level).

Detailed fixes: d31_recommendation.md · top locations in Appendix A, every location in findings.md.

Do you agree with this assessment?

D34 · Knowledge Freshness1.8 / 10Critical✓ Tool-verified

What it measures: Whether anyone still has living knowledge of each file, or it has been orphaned — last understood long ago by someone now gone quiet. The sibling of the bus factor: D16 asks who owns it, D34 asks whether anyone still knows it.

Method: File orphaning as total living-knowledge decay below one focused-commit's worth within a year, computed per-file from the D16 decay model. Exhaustive, deterministic over fixed history.

Maturity: Documented → Verified → Prevented · effective 1.8 / 10 · rule-coverage 100% · ceiling Documented

409 of 500 significant source file(s) are orphaned — their living knowledge has decayed to nothing, so no one currently understands them. The largest is wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala. Counted over 500 of the 1152 production source files in this repository: the rest are under the ~2,400-byte size floor this dimension measures over.

Most significant orphaned file · ×3wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala

Concentrated knowledge decay

What to do

Resolve the 3 Most significant orphaned file finding(s) in Knowledge Freshness — start with EngineFunctionEvaluators.scala, WorkflowActor.scala, S3FileSystemProvider.java. — One of this dimension's main actionable groups (3 recommendation-level).
Resolve the 1 Concentrated knowledge decay finding(s) in Knowledge Freshness. — One of this dimension's main actionable groups (1 recommendation-level).

Detailed fixes: d34_recommendation.md · top locations in Appendix A, every location in findings.md.

Do you agree with this assessment?

D35 · Change Coupling10.0 / 10Adequategated by 4 critical findings✓ Tool-verified

What it measures: Whether files that change together actually belong together — pairs that repeatedly co-change in git history despite having no explicit code dependency, surfacing the hidden/logical coupling (and boundaries in the wrong place) a static scan can't see.

Method: Pairwise co-occurrence over the per-commit file sets in git history (production source only — tests and generated dropped): Degree-of-Coupling = shared ÷ min individual revisions, reported above noise floors (each file ≥10 revisions, ≥5 shared commits, ≥50% strength); sweeping commits excluded. Deterministic over fixed history.

Coverage: Population: PRODUCTION source files only — test and generated files are dropped before pairing, so a class co-changing with its own test (trivially ~100%) can't drown the real production↔production coupling. Pairs ranked by Degree-of-Coupling. A non-source file is never a coupling PARTICIPANT either: documentation, schemas, config and data files are dropped with the rest, so a code↔docs pair — a command and the reference page that restates it — is not reported however strongly the two co-change; nor is coupling that runs THROUGH a build step or config file.

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Documented

Strongest change-coupling: MetadataSqlDatabase.scala↔MetadataDatabaseAccess.scala 100%; Dependencies.scala↔Merging.scala 90%; CallCachingSlickDatabase.scala↔CallCache.scala 64%

Boundary-crossing change coupling: MetadataSqlDatabase.scala ↔ MetadataDatabaseAccess.scala · ×4database/sql/src/main/scala/cromwell/database/sql/MetadataSqlDatabase.scala

Change coupling: Dependencies.scala ↔ Merging.scala · ×2project/Dependencies.scala

What to do

Resolve the 4 Boundary-crossing change coupling finding(s) in Change Coupling — start with MetadataSqlDatabase.scala (2), CallCachingSlickDatabase.scala, MetadataRouteSupport.scala. — One of this dimension's main actionable groups (4 issue-level).
Resolve the 2 Change coupling finding(s) in Change Coupling — start with Dependencies.scala, GcpBatchAsyncBackendJobExecutionActor.scala. — One of this dimension's main actionable groups (2 warning-level).

Detailed fixes: d35_recommendation.md · top locations in Appendix A, every location in findings.md.

Do you agree with this assessment?

D36 · Supply-chain Provenance & Signing0.0 / 10Critical✓ Tool-verified

What it measures: Whether the build pipeline provides supply-chain integrity — generated provenance/attestation, signed artifacts (cosign/sigstore), an SBOM, and pinned build actions. Presence of the configuration, not a runtime guarantee.

Method: Supply-chain provenance/signing read deterministically from CI/build config (.github/workflows, .gitlab-ci.yml, azure-pipelines, Jenkinsfile, .circleci) + the release surface: four signals — generated provenance/attestation (SLSA/in-toto/actions-attest), artifact signing (cosign/sigstore/gitsign), an SBOM (syft/sbom-action/*.spdx.json/*.cdx.json), and SHA-pinned build actions — scored 10·present/denom. NotApplicable without a build pipeline. Detects configuration presence, not runtime enforcement.

Maturity: Documented → Verified → Prevented · effective 0.0 / 10 · rule-coverage 100% · ceiling Documented

0/4 supply-chain integrity signals present (provenance, signing, SBOM, pinned actions).

REDACTED

+ 2 more group(s) — more in Appendix A; the complete list is findings.md.

What to do

Resolve the 1 REDACTED finding(s) in Supply-chain Provenance & Signing. — One of this dimension's main actionable groups (1 warning-level).
Resolve the 1 REDACTED finding(s) in Supply-chain Provenance & Signing. — One of this dimension's main actionable groups (1 warning-level).
Resolve the 1 REDACTED finding(s) in Supply-chain Provenance & Signing. — One of this dimension's main actionable groups (1 warning-level).

Detailed fixes: d36_recommendation.md · top locations in Appendix A, every location in findings.md.

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D44 · Platform End-of-Life10.0 / 10Exemplary✓ Tool-verified

What it measures: Whether anyone still ships security patches for the platform this repository RUNS ON — the runtime it pins and the framework majors its own constraints hold it to. Separate from D12 because the question differs: a current Django on an end-of-life Python is perfectly up to date and completely unsupported, and the fix is a migration rather than a version bump. What the repository says it merely SUPPORTS is never charged.

Method: End-of-life PLATFORM read from the repository's own declarations and graded against a FROZEN, dated table of vendor support dates — no network, no feed, no API, so this dimension answers identically inside a closed scan fence. Two subjects: a RUNTIME the project pins (a single or all-end-of-life TargetFramework, a .nvmrc or .python-version, a requires-python CAP) and a FRAMEWORK major a dependency constraint cannot move off (a caret, tilde or exact version; `vue@^2.7.16` pins Vue 2). A FLOOR is deliberately never charged — `requires-python = ">=3.8"` states what a package SUPPORTS, not what it runs on — and a multi-target project is charged only when EVERY target is out of support. Runtime 4.0/product capped 8.0, framework 1.5 capped 4.5. The table is safe to freeze because a statement about support that ended in the past cannot become false: it loses recall as it ages, never precision, and a test asserts every entry predates the freeze date. Disjoint from D31 (a container image's OS layer) and D29 (the toolchain a CI workflow installs). Abstains when the repository declares no platform this pass reads — never scores it clean.

Maturity: Documented → Verified → Prevented · effective 10.0 / 10 · rule-coverage 100% · ceiling Documented

0 end-of-life runtime(s) and 0 end-of-life framework(s), read from 0 platform declaration(s) and 3 dependency declaration(s). This dimension reads what the repository says about ITSELF — a pinned target framework, a version file, a capped requires-python, a Rust toolchain pin, a framework major a constraint cannot move off. A FLOOR is deliberately never charged: `requires-python = ">=3.8"` states what the package SUPPORTS, not what it runs on, and a well-maintained library declares exactly that while running its own CI on a current release. The end-of-life facts are FROZEN and dated, so this dimension needs no network and answers identically inside a closed scan fence; as the table ages it loses recall and never precision, because a statement about support that ended in the past cannot become false. The OS layer of a container image is D31's question and the toolchain a CI workflow installs is D29's; this row is neither.

✓ On the Gold path — maintain.

Detailed fixes: d44_recommendation.md.

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Frontend & cross-cutting dimensions

R = React/JS · M = Maturity · P = Readiness.

AX10 · Code composition9.6 / 10Exemplary✓ Tool-verified

Other · Architecture — How the codebase splits by code ROLE — domain, application, infrastructure, test, generated. The significance map behind the knowledge/coupling weighting, and a DDD signal in its own right: a thin domain core under fat infrastructure is the anemic-domain smell, quantified. How each file's role is decided, because the split is only as good as that: a generated name or a build-output tree makes it Generated, a test project makes it Test, and otherwise the file's NAMESPACE and PATH words are matched against fixed vocabularies in a fixed ORDER — domain, then infrastructure, then application — so a file whose words hit two layers is counted under the earlier one. A production file matching none of them counts as application, so that share reads 'application or unclassified' rather than a measured application layer. Roles come from naming convention, never from what the code does. On this repository the split was taken from the source tree on disk rather than from a loaded .NET workspace, so a file's role is decided by its PATH segments alone — no declared namespace was available to add to the evidence — and generated output is excluded from the census entirely rather than counted as a generated share.

Method: Roslyn line-count by code ROLE: every source file classified Domain/Application/Infrastructure/Test/Generated by namespace + path convention (the shared CodeRoleClassifier), then significant lines summed per role. Deterministic; the advisory score is the business-logic (domain+application) share of production code.

Coverage: Population: ALL source files, each bucketed into ONE of five roles (Domain/Application/Infrastructure/Test/Generated) by namespace + path convention — a file whose layer isn't named in the convention falls to Application (the neutral default), and the split is line-count, not semantic depth or business value.

What to do

The domain core is a small share of production code, but most of the rest matched no layer vocabulary at all — so this is not yet an anemic-domain finding. The namespace/path convention could not place that code, which makes the composition above a statement about the naming, not about the design. Name the layers (or check that the repository's conventions differ from the ones this check knows) before reading a thin domain into it.

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AX3 · Project dependency cycles10.0 / 10Exemplary✓ Tool-verified

Other · Architecture — Whether the project-reference graph is acyclic (cycles block independent build/deploy and signal eroding boundaries).

Method: Project reference cycles via elementary-DFS over real .csproj references, using the engine shared with D5/D7; cyclic versus acyclic. Exhaustive, deterministic.

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AX4 · Dependency direction10.0 / 10Exemplary✓ Tool-verified

Other · Architecture — Whether dependencies point inward (Domain ← Application ← Infrastructure/Web) — the clean-architecture dependency rule, checked across the project graph.

Method: Layer violations by name-segment inference (Domain/Core to Application to Infrastructure/Web) over the project-reference graph. Exhaustive over all projects, deterministic.

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M1 · Documentation (README)4.5 / 10Weak✓ Tool-verified

Maturity · Maturity — Whether the repo and its projects have a README, and whether it's substantive and current.

Method: Filesystem scan: README presence, word count, and headings for depth; git history for staleness. Exhaustive across root and project dirs, deterministic.

122 code files changed in the last 6 months but the README was not touched — it may no longer reflect the system.

What to do

Add a build/run (quick start) section to the root README — the first thing a newcomer needs.
Add a 'Testing' section to the root README — how to run the test suite.
Add an 'Architecture' / 'How it works' section to the root README — the high-level shape.
Add a README to the 2 of 2 project(s) that lack one — worth up to 2 pts.
Review the README against recent changes; refresh the parts that drifted.

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M2 · Architecture documentation5.0 / 10Adequate✓ Tool-verified

Maturity · Maturity — Whether key decisions (ADRs) and the high-level shape (C4/diagrams) are written down.

Method: Filesystem scan: ADR folder/naming conventions or content, plus Mermaid/PlantUML/C4/architecture.md discovery. Exhaustive, deterministic.

No Architecture Decision Records found — no conventional ADR directory, no numbered `NNNN-title` documents in any markup this check reads, and nothing ADR-shaped by content. Design rationale recorded elsewhere (a design-notes tree, a mailing list, pull-request discussion) is not visible to this check and is not re-findable per decision, so a future maintainer cannot ask why one choice was made and get an answer.

What to do

Record significant decisions one document per decision — dated, stating the context, the decision and its consequences — and keep them together wherever your design docs already live (a conventional `docs/adr/` tree, with each file named `NNNN-title` in whatever markup those docs already use, is the most discoverable form).

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M3 · Folder & project structure10.0 / 10Exemplary✓ Tool-verified

Maturity · Maturity — Whether the repo is organised deliberately — src/test separation and consistent project naming.

Method: Filesystem scan: src/test folder separation and namespace-prefix consistency (majority RootNamespace agreement). Exhaustive across projects, deterministic.

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M4 · Documentation accuracy10.0 / 10Exemplary◐ Sampled · advisory

Maturity · Maturity — Whether the README actually describes the code that exists (LLM-judged, advisory).

Method: Judged by language model at low temperature: README accuracy versus actual projects, within a disclosed tolerance. Advisory, not a measured number.

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P1 · CI/CD gates10.0 / 10Exemplary○ Nothing flagged

Readiness · Readiness — Whether an automated pipeline builds and tests every change.

Method: Filesystem scan: CI workflow files (.github/workflows, .gitlab-ci.yml, etc.) for build and test stages. Exhaustive, deterministic.

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P2 · Observability9.0 / 10Exemplary✓ Tool-verified

Readiness · Readiness — Whether the code is diagnosable in production — structured logging, tracing/metrics, health checks.

Method: Filesystem/Roslyn scan: structured-logging frameworks (Serilog, NLog), OpenTelemetry, and health-check endpoint patterns. Exhaustive, deterministic.

What to do

Add a health-check endpoint (Spring Boot Actuator's /actuator/health, or a /health route) so orchestrators and load balancers can probe liveness/readiness.

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P3 · Security & performance tooling0.0 / 10Critical✓ Tool-verified

Readiness · Readiness — Whether SAST, secret/dependency scanning and performance benchmarking are wired in (presence, not runtime).

Method: Filesystem scan: SAST configuration, dependency-update automation, secret scanning, and a benchmark harness or benchmark step — in this repository's own ecosystem. Exhaustive, deterministic.

No static application security testing detected. For this repository's stack, add scalafix or scapegoat (or `semgrep --config=auto`, which runs on any language) as a CI step. What was searched, so you can tell an absence from a miss: the 20131 CI workflow file(s) in this repository, and the scanner and linter configuration checked in beside them. A scan that runs outside CI, one configured in your forge's web UI rather than in a committed file, or a tool whose name is none of those this check carries, is not seen — if that is your case the row is wrong, and saying so is more useful than adding a second scanner.

What to do

Add a SAST step to CI running what this repository's stack ships: scalafix or scapegoat — or `semgrep --config=auto`, which runs on any language — so a security regression fails the build instead of landing.
Enable Dependabot/Renovate or a dependency-review gate.
Add gitleaks/trufflehog in CI to block PRs that introduce committed secrets.

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P4 · Deployment & Rollback10.0 / 10Exemplary✓ Tool-verified

Readiness · Readiness — Whether releases are automated and safely reversible (probes, rolling updates, approval gates) — from manifests/pipeline files, not the live environment.

Method: Filesystem scan: deployment manifests/IaC (K8s YAML, Helm, Terraform) for rolling updates, probes, approval gates, migration hooks. Exhaustive, deterministic.

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P6 · Release Hygiene10.0 / 10Exemplary✓ Tool-verified

Readiness · Readiness — Whether releases are traceable — a maintained changelog and explicit version stamping.

Method: Filesystem scan: changelog file presence and version tags in csproj or git tags. Exhaustive, deterministic.

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P8 · Schema migrations10.0 / 10Exemplary○ Nothing flagged

Readiness · Readiness — Whether database schema changes go through versioned migrations rather than being auto-created from the model at startup.

Method: Roslyn scan: EF Core DbContext for a versioned migrations directory versus bare EnsureCreated usage; off .NET, a file scan of dependency manifests, migration histories (Flyway, Liquibase, Alembic, Django, Rails, Prisma, TypeORM, Knex/Sequelize, golang-migrate, goose, Laravel, Doctrine, Diesel/sqlx) and schema auto-create in production source or config. Exhaustive, deterministic.

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S1 · Web-Security Posture6.0 / 10Adequate✓ Tool-verified

Other · Security — Only what this repository's own non-C# files could be read for was assessed — markup this repository SHIPS is scored for third-party script integrity whether or not the repository serves it itself, since a page handed to a consumer runs in that consumer’s origin — and because this repository commits the configuration that serves its own HTTP surface, that configuration could be read in full for the security response headers it sets. Nothing else in this dimension was assessed: the transport, cookie, input-validation and crypto controls are read from a source model that was not loaded for this repository’s language, so their absence here is not a finding about this repository.

Method: Roslyn plus filesystem scan: HSTS/security headers, secure cookies, input validation, middleware order, weak crypto (MD5/SHA1/DES); HTTPS-metadata context-aware. Deterministic.

`https://www.gstatic.com/charts/loader.js` is executed by this page with no Subresource Integrity. Whoever can answer that request — the CDN, anyone who compromises it, anyone on the network path — runs arbitrary script in this page's origin, with its session. The URL also names no version, so it resolves to whatever that origin serves at fetch time — the executed bytes can change with nobody touching this repository. 2 such include(s) across the repository's markup. — engine/src/main/resources/workflowTimings/workflowTimings.html:4
No Content-Security-Policy / X-Frame-Options / X-Content-Type-Options configuration found — defense in depth, even when a reverse proxy could set them. This is reported because `application.conf` is committed to this repository and declares the server that serves it, so the configuration that would carry these headers is in this repository and was read in full. (−2.0 on this card.) — CromIAM/src/main/resources/application.conf:30

What to do

Pin third-party scripts and verify them: name an exact version in the URL and add an `integrity="sha384-…"` hash alongside `crossorigin="anonymous"` (both are required — an integrity hash on a cross-origin script without `crossorigin` is not evaluated, it blocks the script). Where the vendor ships a continuously-updated loader and publishes no stable hash (tag managers, analytics, chat widgets), Subresource Integrity is not available: constrain it instead with a `Content-Security-Policy` that names the exact origins allowed to execute, and drop the script from the pages that do not need it. Where the page is shipped inside a package that others host, prefer vendoring the asset and serving it from the app’s own origin, so no consumer inherits a third-party dependency they did not choose.
Set security response headers on the surface this repository serves: an `add_header` directive per header in the nginx/Caddy/Apache config, a `_headers` / `vercel.json` / `netlify.toml` entry for a static host, or `helmet()` in the HTTP server. `Content-Security-Policy` is the one that pays for itself first — it is what contains an injected script once one reaches the page — followed by `X-Content-Type-Options: nosniff` and a frame policy (`X-Frame-Options: DENY`, or CSP `frame-ancestors`). Where the app is served from a build container, the header configuration belongs in the image beside the built assets, so it ships with them rather than depending on where it lands.

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Reference — by lens

The score is the rank-weighted fold of these lenses (worst-heaviest), each including its meta-dimensions; a lens with a Critical contributor is capped at Fair (its band reads "gated by …") and is never the strongest area however high its average.

Lens	Score	Rating	Impact
Code Health	87%	Strong	Strongest area.
Architecture	85%	Adequate — gated by D26	Capped at Fair by a Critical contributor — resolve it before relying on this lens.
Maturity	65%	Adequate — gated by D34	Capped at Fair by a Critical contributor — resolve it before relying on this lens.
Readiness	65%	Adequate — gated by P3	Capped at Fair by a Critical contributor — resolve it before relying on this lens.
Security	51%	Adequate — gated by D29, D36	Capped at Fair by a Critical contributor — resolve it before relying on this lens.

Not evidenced — 4 control(s) we could not find positive evidence for

These checks grade a working control, and the repository shows no evidence of one. That is deliberately not scored as a zero: a repository cannot show an ops runbook, a database TTL or an infrastructure-side audit log, so absence of evidence here is not evidence the control is missing. It is also not a statement that the check is irrelevant to this codebase — the thing it grades applies; we just could not see it. Excluded from the score either way.

C3 Audit Trail — Not assessed: these audit controls are read from a source model (declarative annotations, request middleware, entity/column names, guard methods) that was not loaded for this repository — because the repository is written in a language this check does not yet model, or because its projects failed to load. Absence of an idiom this check recognises is NOT evidence that this repository lacks audit controls: it may implement them entirely in its own ecosystem. This is a gap in the analyzer's language coverage, not a finding about this repository.
C4 Data Retention — Not assessed: these retention controls are read from a source model (declarative annotations, request middleware, entity/column names, guard methods) that was not loaded for this repository — because the repository is written in a language this check does not yet model, or because its projects failed to load. Absence of an idiom this check recognises is NOT evidence that this repository lacks retention controls: it may implement them entirely in its own ecosystem. This is a gap in the analyzer's language coverage, not a finding about this repository.
C5 Data-Subject Rights — Not assessed: these data-subject rights controls are read from a source model (declarative annotations, request middleware, entity/column names, guard methods) that was not loaded for this repository — because the repository is written in a language this check does not yet model, or because its projects failed to load. Absence of an idiom this check recognises is NOT evidence that this repository lacks data-subject rights controls: it may implement them entirely in its own ecosystem. This is a gap in the analyzer's language coverage, not a finding about this repository.
P5 DR & Backup — not evidenced — repo shows no backup/RTO/RPO controls; absence of evidence is not evidence of a working control

Not included — 80 check(s) not relevant to this codebase

These checks had nothing to measure here (no tests, no git history, the codebase is small, or the architecture style doesn't apply), so they're omitted above rather than scored low.

AC1 Text alternatives — Frontend below the scale floor (8 DOM element(s) < 25) — too little surface to assess accessibility.
AC2 Forms & labels — Frontend below the scale floor (8 DOM element(s) < 25) — too little surface to assess accessibility.
AC3 Page structure — Frontend below the scale floor (8 DOM element(s) < 25) — too little surface to assess accessibility.
AC4 Keyboard semantics — Frontend below the scale floor (8 DOM element(s) < 25) — too little surface to assess accessibility.
AC5 ARIA correctness — Frontend below the scale floor (8 DOM element(s) < 25) — too little surface to assess accessibility.
AC6 Visual & motion safety — Frontend below the scale floor (8 DOM element(s) < 25) — too little surface to assess accessibility.
AC7 A11y enforcement — Frontend below the scale floor (8 DOM element(s) < 25) — too little surface to assess accessibility.
AX1 Captive dependencies — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
AX2 Stateful singletons — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
AX5 Architecture & structure — not assessed — architecture style/structure is computed from a project graph (projects, types, module namespaces) that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
AX6 Interface segregation — not assessed — interface segregation is computed over a type surface that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
AX7 Slice cohesion — not applicable — not a vertical-slice architecture
AX8 Test isolation — no test/production split to check
AX9 CQS / query purity — no CQRS query handlers detected — query purity is not applicable to this codebase
AXB2 Runtime readiness — Advisory — this card reports evidence and never carries a score, so there is nothing missing here.
AXR1 Runtime accessibility — compose up failed (exit 18 — an image could not be pulled) — postgresql-db Pulling mysql-db Pulling mariadb-db Pulling postgresql-db Error Get "https://registry-1.docker.io/v2/": Forbidden mariadb-db Error Get "https://registry-1.docker.io/v2/": Forbidden mysql-db Error Get "https://registry-1.docker.io/v2/": Forbidden Error response from daemon: Get "https://registry-1.docker.io/v2/": Forbidden; the earlier `compose pull` step reported: cromwell-test Skipped - No image to be pulled postgresql-db Pulling mysql-db Pulling mariadb-db Pulling mysql-db Error Get "https://registry-1.docker.io/v2/": Forbidden postgresql-db Error context canceled mariadb-db Error context canceled Error response from daemon: Get "https://registry-1.docker.io/v2/": Forbidden; the runtime sandbox reaches registries only through the in-fence pull-through mirror, so an image the mirror does not carry cannot be fetched — this is a limit of our sandbox, not of your stack; runtime evidence skipped This is a statement about this run, not a statement about your application: nothing here says the surface is inaccessible, only that it was never rendered.
C1 Data Protection — Not assessed: these personal data controls are read from a source model (declarative annotations, request middleware, entity/column names, guard methods) that was not loaded for this repository — because the repository is written in a language this check does not yet model, or because its projects failed to load. Absence of an idiom this check recognises is NOT evidence that this repository lacks personal data controls: it may implement them entirely in its own ecosystem. This is a gap in the analyzer's language coverage, not a finding about this repository.
C2 Access Controls — Not assessed: these authorization controls are read from a source model (declarative annotations, request middleware, entity/column names, guard methods) that was not loaded for this repository — because the repository is written in a language this check does not yet model, or because its projects failed to load. Absence of an idiom this check recognises is NOT evidence that this repository lacks authorization controls: it may implement them entirely in its own ecosystem. This is a gap in the analyzer's language coverage, not a finding about this repository.
D10 Test Quality — ~72285 lines of test source are present (.scala, .py) but no test cases reached the test census for this repository — no test root we could resolve declared them, or the files we read declare no cases in a test framework we recognise — so skipped/assertion-free tests couldn't be counted. Not scored — this is a gap in the analyzer, not a finding about this repository.
D11 Test Reliability — Test reliability not included — the .scala suite was found but not re-run
D12 Dependency Hygiene — Dependency Hygiene incomplete (time budget)
D18 Solution Shape — D18 scores the shape of a .NET solution; this repository has no .NET solution or project files, so the dimension does not apply.
D22 Internal API Consistency — The exposed public-API surface could not be collected — no C#/VB projects loaded.
D23 Boundary Type-Coupling — No bounded-context organisation was detected either — neither a context-shaped layout nor 2+ sibling source directories each declaring an aggregate root. Declaring this codebase's bounded contexts (≥2) would let cross-boundary type coupling be assessed. Declare them in `.codehealth/config.yaml` at the repository root (create it if absent), mapping each context name to the module-path or namespace prefixes that belong to it — e.g. `architecture:` → `contexts:` → `Billing: ["src/billing", "Acme.Billing"]`, `Catalog: ["src/catalog", "Acme.Catalog"]`.
D24 Comment Value — No inline comments to assess — comment value is not applicable here.
D25 ADR Conformance — no ADRs to check
D27 Navigability — symbol resolution incomplete — navigability not assessed
D30 Dependency Vulnerabilities — Scanner failed to run — not a clean result
D32 Data Compliance (PII/GDPR) — No personal data was found crossing a boundary the PII/GDPR ruleset checks — nothing written to a log or console sink, placed in a URL or query string, or persisted to browser storage. That is a clean result for the LEAK surface only: this ruleset detects personal data escaping, it does not inventory the personal data a repository holds, so it is not evidence that this repository has no personal-data surface. The personal-data map (Appendix C) and the C1-C5 compliance cards are what speak to that.
D37 Vulnerability-disclosure Policy — No vulnerability-disclosure policy file found (SECURITY.md/.markdown/.rst/.txt at root or under .github/.forgejo/.gitea/docs, .well-known/security.txt). A coordinated-disclosure policy may live off-repo, so this is not evidenced rather than failed.
D39 IL Efficiency — D39 measures the IL emitted by a .NET build; this repository has no .NET solution or project files, so the dimension does not apply.
D40 Network Egress Confinement — No Kubernetes/orchestration workloads found in the repository manifests; network egress policy is a cluster-native control that may live at the platform/firewall layer, so there is nothing to assess here.
D41 Kernel & Syscall Confinement — No Kubernetes/orchestration workloads found in the repository manifests; seccomp/AppArmor/SELinux confinement is a workload-level control, so there is nothing to assess here.
D42 Runtime Threat Enforcement — No Kubernetes/orchestration workloads found in the repository manifests; runtime threat-detection and admission-control policy are cluster-level controls, so there is nothing to assess here.
D43 Malicious Dependencies — Scanner failed to run — not a clean result
D5 Coupling — Not applicable — this Maven build ships 1 production module(s), so there is no coupling BETWEEN modules to measure. (Its test and non-production modules are not part of the shipped graph.)
D7 Architectural Integrity — no checkable ADRs, and no project-reference graph for the cycle pass to read — so this dimension makes no claim about dependency cycles in either direction (where this repository's language has an import-cycle lens, cycles are reported there). Architectural integrity not assessed
D8 Code Coverage — Coverage not included — suite not readable by the collector
DM1 Domain Modelling — applicable but not scored (2 signals for this style, 2 needed — the count is met but a required primary signal is absent): 1640 value object(s); 19 domain event(s); its domain events are published by services or handlers — no domain entity raises one
ED1 Event-Driven — not scored — this repository shows none of the 3 signals this lens looks for
ED5 Idempotency — This check finds retry-prone mutations (command handlers and message/event consumers) by walking the repository's declared types, and none was loaded here, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
ES1 Event Sourcing — not scored — this repository shows none of the 3 signals this lens looks for
GD1 Unfinished & placeholder code — no source files were read — this check reads C# syntax, and none was loaded for this repository. That is a limit of the analyzer, not a finding about your code.
IC1 Incompleteness & stubs — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
P10 Library API & versioning — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
P12 CI test-gate honesty — Reported, not scored — this card publishes what the CI gate does with the test inventory rather than grading it. The findings above are its output.
P7 Outbound HTTP resilience — not applicable — no HTTP server, API framework or worker entry point was found in the JVM, JavaScript/TypeScript, Python source, so there is no service whose uptime a failing dependency could take down
P9 Domain vs controller coverage — no coverage report found on disk — produce a coverage report in a standard format (`addSbtPlugin("org.scoverage" % "sbt-scoverage" % "<version>")` in `project/plugins.sbt`, then `sbt clean coverage test coverageReport`) and commit it — a hosted scan measures a clone of the repository, so a report that exists only in a working tree, a CI runner's or your own, never reaches it; the artefact is commonly gitignored, so `git add -f` that one file (or un-ignore its path) and commit it alongside the code it measures, or wire coverage collection into CI, to enable this cross-layer check
PF1 Benchmark discipline — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
PF2 Allocation hygiene — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
PF3 Async & latency hygiene — Sync-over-async was not assessed: this repository's async code is written in Scala, whose blocking calls this check does not model yet. That is a gap in the analyzer's language reach, not a finding about your code.
X1 Async correctness — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
X10 Duplicated predicate — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
X12 Unreachable branch — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X13 Undrained process stream — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X14 Bypassable address classification — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X15 Unvalidated length from an untrusted reader — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X16 Unfloored truncation loop — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X17 Uncapped recursion over a caller-supplied document — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X18 Disposal-pattern correctness — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X19 Unrestored process-global state — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X2 Cancellation propagation — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
X20 Mistyped argument guard — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X21 Side-effecting pattern guard — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X22 Contradicted release guard — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X23 Unguarded diagnostic materialisation — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X24 Document value interpolated into markup unescaped — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X25 Inert configuration knob — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X26 Unsynchronised callback handoff — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X27 Collection changed while being enumerated — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X28 Index access outside its own emptiness guard — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X29 Per-element action decided by a fixed element — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X3 Exception handling — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
X30 Support guard that admits what it rejects — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X32 Type resolved by simple name across every loaded assembly — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X4 Structured logging — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
X5 Nullable reference types — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
X6 Hand-rolled structured-format parsing — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
X7 Silent fallback defaults — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
X9 Subsumed condition operand — Advisory — this card reports evidence and never carries a score, so there is nothing missing here.

Appendix A — Findings (grouped)

The findings behind the scores, grouped by severity, then by dimension and kind. The high-severity issues are enumerated in full below; items per group are capped at 25 with any overflow stated explicitly per group, never silently truncated. The complete machine-readable list of every finding (all severities) is the companion findings.md in this report's bundle.

Critical — 58 finding(s)

D29 · Static Analysis (SAST) · REDACTED

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+ 9 more in this group — see findings.md.

D29 · Static Analysis (SAST) · REDACTED

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D28 · Secrets (history) · REDACTED · ×6

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D31 · IaC & Container Security · High IaC · ×6

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D35 · Change Coupling · Boundary-crossing change coupling · ×4

Boundary-crossing change coupling: MetadataSqlDatabase.scala ↔ MetadataDatabaseAccess.scala database/sql/src/main/scala/cromwell/database/sql/MetadataSqlDatabase.scala — `database/sql/src/main/scala/cromwell/database/sql/MetadataSqlDatabase.scala` (context database) and `services/src/main/scala/cromwell/services/metadata/impl/MetadataDatabaseAccess.scala` (context services) sit in DIFFERENT parts of the tree yet change together 100% of the time (41 of the 41 commits that touched whichever of the two files changed less often, counting a file under its earlier names as well — a repo-wide or module-wide sweep is evidence about the sweep rather than about any pair inside it and is left out of BOTH sides of this ratio, while a dependency bump, a formatter/rename sweep, or a commit whose edit to one of the two files was a tool directive such as //go:generate or whitespace only is left out of the shared count ONLY, so the two sides are not taken over identical commit sets) — the bounded-context boundary may be in the wrong place, or one context is leaking into the other. This is the behavioural boundary violation a static scan can't see. You can check this without leaving the row: of the 41 shared commits counted here, the most recent 3 are `f0bf524f` CTM-4 Remove metadata query row limit (#7878); `c4093a0a` AN-214 Redirect workflow existence queries from metadata to summary (…; `af9660ee` WX-1110[risk=low] Added endpoint to fetch failed tasks by root workfl… — run `git show` on any of them.
Boundary-crossing change coupling: CallCachingSlickDatabase.scala ↔ CallCache.scala database/sql/src/main/scala/cromwell/database/slick/CallCachingSlickDatabase.scala — `database/sql/src/main/scala/cromwell/database/slick/CallCachingSlickDatabase.scala` (context database) and `engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCache.scala` (context engine) sit in DIFFERENT parts of the tree yet change together 64% of the time (9 of the 14 commits that touched whichever of the two files changed less often, counting a file under its earlier names as well — a repo-wide or module-wide sweep is evidence about the sweep rather than about any pair inside it and is left out of BOTH sides of this ratio, while a dependency bump, a formatter/rename sweep, or a commit whose edit to one of the two files was a tool directive such as //go:generate or whitespace only is left out of the shared count ONLY, so the two sides are not taken over identical commit sets) — the bounded-context boundary may be in the wrong place, or one context is leaking into the other. This is the behavioural boundary violation a static scan can't see. You can check this without leaving the row: of the 9 shared commits counted here, the most recent 3 are `39c03e5d` [CTM-133] Reverse call-caching order and not check old entries (#7834); `9b396aac` Fix call cache checks in case of cache invalidation w/ test [CROM-660…; `2d8a0a1b` WIP — run `git show` on any of them.
Boundary-crossing change coupling: MetadataSqlDatabase.scala ↔ ReadDatabaseMetadataWorkerActor.scala database/sql/src/main/scala/cromwell/database/sql/MetadataSqlDatabase.scala — `database/sql/src/main/scala/cromwell/database/sql/MetadataSqlDatabase.scala` (context database) and `services/src/main/scala/cromwell/services/metadata/impl/ReadDatabaseMetadataWorkerActor.scala` (context services) sit in DIFFERENT parts of the tree yet change together 58% of the time (7 of the 12 commits that touched whichever of the two files changed less often, counting a file under its earlier names as well — a repo-wide or module-wide sweep is evidence about the sweep rather than about any pair inside it and is left out of BOTH sides of this ratio, while a dependency bump, a formatter/rename sweep, or a commit whose edit to one of the two files was a tool directive such as //go:generate or whitespace only is left out of the shared count ONLY, so the two sides are not taken over identical commit sets) — the bounded-context boundary may be in the wrong place, or one context is leaking into the other. This is the behavioural boundary violation a static scan can't see. You can check this without leaving the row: of the 7 shared commits counted here, the most recent 3 are `f0bf524f` CTM-4 Remove metadata query row limit (#7878); `af9660ee` WX-1110[risk=low] Added endpoint to fetch failed tasks by root workfl…; `32d5d0cb` Archiving scale fixes: Pin fetchSize for DB stream, better metric rep… — run `git show` on any of them.
Boundary-crossing change coupling: MetadataRouteSupport.scala ↔ ReadDatabaseMetadataWorkerActor.scala engine/src/main/scala/cromwell/webservice/routes/MetadataRouteSupport.scala — `engine/src/main/scala/cromwell/webservice/routes/MetadataRouteSupport.scala` (context engine) and `services/src/main/scala/cromwell/services/metadata/impl/ReadDatabaseMetadataWorkerActor.scala` (context services) sit in DIFFERENT parts of the tree yet change together 50% of the time (6 of the 12 commits that touched whichever of the two files changed less often, counting a file under its earlier names as well — a repo-wide or module-wide sweep is evidence about the sweep rather than about any pair inside it and is left out of BOTH sides of this ratio, while a dependency bump, a formatter/rename sweep, or a commit whose edit to one of the two files was a tool directive such as //go:generate or whitespace only is left out of the shared count ONLY, so the two sides are not taken over identical commit sets) — the bounded-context boundary may be in the wrong place, or one context is leaking into the other. This is the behavioural boundary violation a static scan can't see. You can check this without leaving the row: of the 6 shared commits counted here, the most recent 3 are `dde735a8` WX-1784 Compute cost from metadata (#7537); `f0a05ca4` WX-1783 Dummy Cost API (#7508); `af9660ee` WX-1110[risk=low] Added endpoint to fetch failed tasks by root workfl… — run `git show` on any of them.

D13 · REDACTED Scanning · Leaked secret · ×1

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Serious — 233 finding(s)

D17 · Explicit Debt · TodoComment · ×78

TodoComment CromIAM/src/test/scala/cromiam/webservice/SwaggerUiHttpServiceSpec.scala:47 — // TODO: Re-common-ize swagger out of cromwell's engine and reuse. — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment backend/src/main/scala/cromwell/backend/OutputEvaluator.scala:55 — // TODO WOM: coerceRawValue should return an ErrorOr — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment backend/src/main/scala/cromwell/backend/io/DirectoryFunctions.scala:44 — // TODO: WOM: WOMFILE: How did a glob get here? Should this link into glob functions to list the globs? — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment backend/src/main/scala/cromwell/backend/standard/StandardExpressionFunctions.scala:29 — // TODO: Once we figure out premapping and postmapping, maybe we can standardize that behavior. Currently that's the most important feature that subclasses override. — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala:617 — // TODO: Asynchronify — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala:767 — // TODO CWL: Is throwing an exception the best way to indicate command generation failure? — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala:74 — // TODO: this mechanism here is very close to the one in CallCacheHashingJobActorData — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment backend/src/main/scala/cromwell/backend/validation/Containers.scala:61 — // TODO enhance to select the best container from the list if multiple are provided. — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioFileSystemProvider.scala:50 — // TODO: Do NOT convert to a URI. Do soft parsing. — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioFileSystem.scala:12 — //TODO: Use stronger type for CloudNioFileSystemProvider to avoid casting — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/CloudNioPaths.scala:26 — // TODO: softer parsing using Guava UrlEscapers. May also be better to list the providers ourselves if possible. — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment core/src/main/scala/cromwell/core/CromwellGraphNode.scala:6 — // TODO WOM: we could move this into WOM as it's already there for GraphNodes — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala:31 — // TODO: rename column via liquibase — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala:33 — // TODO: rename column via liquibase — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala:35 — // TODO: rename column via liquibase — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala:37 — // TODO: rename column via liquibase — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment database/sql/src/main/scala/cromwell/database/sql/SqlConverters.scala:12 — // TODO: Storing times relative to system zone. Look into db/slick using OffsetDateTime, or storing datetimes as UTC? — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment engine/src/main/scala/cromwell/engine/EngineIoFunctions.scala:20 — // TODO: This is not suited for multi backend / multi filesystem use. Keep local for now to not break local CWL conf tests — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment engine/src/main/scala/cromwell/engine/instrumentation/WorkflowInstrumentation.scala:62 — // * TODO: enforce a terminal state ? — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala:587 — // TODO: Instead of simply logging to Kibana, figure out a way to tell the user what were the errors somehow (maybe through metadata?) — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment engine/src/main/scala/cromwell/engine/workflow/lifecycle/materialization/MaterializeWorkflowDescriptorActor.scala:188 — // TODO WOM: need to decide where to draw the line between language specific initialization and WOM — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment engine/src/main/scala/cromwell/engine/workflow/lifecycle/materialization/MaterializeWorkflowDescriptorActor.scala:575 — // TODO WOM: need access to a "source string" for WomExpressions — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment engine/src/main/scala/cromwell/engine/workflow/lifecycle/materialization/MaterializeWorkflowDescriptorActor.scala:576 — // TODO WOM: ErrorOrify this ? — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment engine/src/main/scala/cromwell/webservice/routes/WomtoolRouteSupport.scala:57 — // TODO: move constants to WebServiceUtils, adopt in PartialWorkflowSources — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment engine/src/test/scala/cromwell/engine/workflow/tokens/JobTokenDispenserActorSpec.scala:509 — // TODO: validate that the probe has left the queue — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
+ 53 more in this group — see findings.md.

D17 · Explicit Debt · FixmeComment · ×9

FixmeComment CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala:31 — // FIXME - getting pathPrefix to shrink this keeps hosing up, there's gotta be some way to do this — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
FixmeComment CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala:115 — // FIXME: Much like CromwellClient see if there are ways of unifying this a bit w/ the mothership — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
FixmeComment CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala:183 — // FIXME: Unify these w/ Cromwell.PartialWorkflowSources (via common?) — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
FixmeComment CromIAM/src/main/scala/cromiam/webservice/CromIamApiService.scala:61 — // FIXME: use workbench-model ErrorReport — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
FixmeComment backend/src/main/scala/cromwell/backend/BackendWorkflowInitializationActor.scala:139 — // FIXME: If a workflow executes jobs using multiple backends, — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
FixmeComment engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala:241 — // FIXME: to handle - page_size, page_token — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
FixmeComment engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala:242 — // FIXME: How to handle next_page_token in response? — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
FixmeComment wdl/model/draft2/src/test/scala/wdl/SampleWdl.scala:8 — // FIXME: Figure out if anything can be removed from cromwell completely or pulled from here — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
FixmeComment wom/src/main/scala/wom/callable/WorkflowDefinition.scala:17 — // FIXME: how to get a meaningful order from the node set ? — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `// REF: #123`), so the task is planned where tasks live and the ticket links back to the code.

D3 · God Classes · FileTooLong · ×7

FileTooLong: actors/GcpBatchAsyncBackendJobExecutionActor.scala supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala — FileTooLong — 960 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 460 over it, 1.92× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
FileTooLong: job/EngineJobExecutionActor.scala engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala — FileTooLong — 851 significant lines (blank, comment-only and punctuation-only lines excluded), about 78% of them inside a single declaration: EngineJobExecutionActor (64-1034). The bar is 500 significant lines; this is 351 over it, 1.70× the bar. Moving the declarations that sit BESIDE it into sibling files will not shorten this file. Extract from INSIDE that declaration instead: lift each cohesive group of its body — the parts that share the same inputs and are named together — into its own unit in a sibling file, and have the original call them.
FileTooLong: standard/StandardAsyncExecutionActor.scala backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala — FileTooLong — 801 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 301 over it, 1.60× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
FileTooLong: execution/WorkflowExecutionActor.scala engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActor.scala — FileTooLong — 682 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 182 over it, 1.36× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
FileTooLong: values/EngineFunctionEvaluators.scala wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala — FileTooLong — 678 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 178 over it, 1.36× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.
FileTooLong: workflow/WorkflowActor.scala engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala — FileTooLong — 567 significant lines (blank, comment-only and punctuation-only lines excluded), about 71% of them inside a single declaration: WorkflowActor (262-860). The bar is 500 significant lines; this is 67 over it, 1.13× the bar. Moving the declarations that sit BESIDE it into sibling files will not shorten this file. Extract from INSIDE that declaration instead: lift each cohesive group of its body — the parts that share the same inputs and are named together — into its own unit in a sibling file, and have the original call them.
FileTooLong: model/WdlNamespace.scala wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlNamespace.scala — FileTooLong — 533 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 33 over it, 1.07× the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them.

D31 · IaC & Container Security · Medium IaC · ×7

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D3 · God Classes · TooManyMethods · ×6

TooManyMethods: BetterFileMethods core/src/main/scala/cromwell/core/path/BetterFileMethods.scala:25 — TooManyMethods — 148 methods. The bar is 30 methods; this is 118 over it, 4.93× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
TooManyMethods: StandardAsyncExecutionActor backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala:86 — TooManyMethods — 69 methods. The bar is 30 methods; this is 39 over it, 2.30× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
TooManyMethods: EngineJobExecutionActor engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala:64 — TooManyMethods — 41 methods. The bar is 30 methods; this is 11 over it, 1.37× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
TooManyMethods: WdlStandardLibraryFunctions wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/WdlStandardLibraryFunctions.scala:24 — TooManyMethods — 36 methods. The bar is 30 methods; this is 6 over it, 1.20× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
TooManyMethods: WdlStandardLibraryFunctionsType wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/WdlStandardLibraryFunctions.scala:526 — TooManyMethods — 35 methods. The bar is 30 methods; this is 5 over it, 1.17× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
TooManyMethods: GcpBatchAsyncBackendJobExecutionActor supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala:153 — TooManyMethods — 34 methods. The bar is 30 methods; this is 4 over it, 1.13× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.

D4 · Code Duplication · Duplicated block (6 lines × 2) · ×6

Duplicated block (6 lines × 2) wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/FileEvaluator.scala:163 — wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/FileEvaluator.scala:163-168 | wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala:75-80 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once. Read the line range as the matched WINDOW rather than a finished unit: at `wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/FileEvaluator.scala:163` it runs out through the closing brace of the declaration holding it and carries on into the declaration that follows — the window is the tail of one member plus the head of the next, so no call can be substituted for those exact lines, and the smallest declaration that contains all of them is the type they sit in. The repeated unit is the member each site sits in: where those members' bodies are the same, move one whole member to the shared location and have the others delegate to it; where the copies are a run of near-identical overloads or wrappers that differ only in their signatures, the repetition IS the run — a one-line delegation has no helper inside it to lift — so generate the run from the set it enumerates, or accept it and keep each member's own documentation with it.
Duplicated block (6 lines × 2) wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala:44 — wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala:44-49 | wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/ValueEvaluator.scala:83-88 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once. Read the line range as the matched WINDOW rather than a finished unit: at `wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala:44` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (6 lines × 2) wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala:50 — wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala:50-55 | wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/ValueEvaluator.scala:89-94 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once. Read the line range as the matched WINDOW rather than a finished unit: at `wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala:50` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (6 lines × 2) wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala:155 — wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala:155-160 | wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala:155-160 — before extracting anything, compare `wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala` and `wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala` as WHOLE FILES: 98% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 1 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. The two sit in different directories, so one cannot simply be deleted in favour of the other while both are reached separately: hoist the shared part into a location both already depend on and have each file call it, and retire whichever file turns out to have no caller of its own left. Extracting one helper per block leaves the fork in place. Read the line range as the matched WINDOW rather than a finished unit: at `wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala:155` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (6 lines × 2) cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/GoogleConfiguration.scala:22 — cloudSupport/src/main/scala/cromwell/cloudsupport/aws/AwsConfiguration.scala:53-58 | cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/GoogleConfiguration.scala:22-27 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. Note first that the copies are not typed on the same thing: the declarations holding them bind `authsByName` to `Map[String, AwsAuthMode]` in one and `Map[String, GoogleAuthMode]` in another, and the duplicated lines use it. The extracted unit therefore needs a parameter type that fits BOTH — their common supertype where they have one, or a new abstraction over them where they do not — and settling that is the step that comes BEFORE the extraction above. Where the two types are deliberately unrelated, the duplication is the price of that separation and the honest resolution is to record the decision rather than to extract.
Duplicated block (6 lines × 2) wom/src/main/scala/wom/types/WomFloatType.scala:31 — wom/src/main/scala/wom/types/WomFloatType.scala:31-36 | wom/src/main/scala/wom/types/WomIntegerType.scala:39-44 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.

D4 · Code Duplication · Duplicated block (5 lines × 2) · ×6

Duplicated block (5 lines × 2) database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala:260 — database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala:260-264 | database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala:273-277 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala:260` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (5 lines × 2) wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala:72 — wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala:72-76 | wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/ValueEvaluator.scala:123-127 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.
Duplicated block (5 lines × 2) supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala:1145 — supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala:1127-1131 | supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala:1145-1149 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice.
Duplicated block (5 lines × 2) supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala:271 — supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala:597-601 | supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala:271-275 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice.
Duplicated block (5 lines × 2) supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala:286 — supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala:612-616 | supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala:286-290 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice.
Duplicated block (5 lines × 2) wom/src/main/scala/wom/types/WomFloatType.scala:38 — wom/src/main/scala/wom/types/WomFloatType.scala:38-42 | wom/src/main/scala/wom/types/WomIntegerType.scala:46-50 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.

D6 · Cohesion (LCOM4) · Low cohesion · ×6

Low cohesion: TesAsyncBackendJobExecutionActor (LCOM4 7) supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala:222 — TesAsyncBackendJobExecutionActor's methods fall into 7 groups that share no field and call none of each other, against a bar of more than 3 for this run (LCOM4, configurable — your repository's bar is the one quoted here). Each group is a set of methods reachable from one another through shared fields or direct calls, so 7 groups means the type has that many internally-connected clusters with nothing tying them together. Types whose shape makes a high count expected — and which would otherwise dominate this list — are excluded before this row is raised, so this is a genuine split candidate rather than a metric reading. It is still a shape, not a defect: confirm the groups match responsibilities you can name before splitting.
Low cohesion: WorkflowDockerLookupActor (LCOM4 6) engine/src/main/scala/cromwell/engine/workflow/WorkflowDockerLookupActor.scala:46 — WorkflowDockerLookupActor's methods fall into 6 groups that share no field and call none of each other, against a bar of more than 3 for this run (LCOM4, configurable — your repository's bar is the one quoted here). Each group is a set of methods reachable from one another through shared fields or direct calls, so 6 groups means the type has that many internally-connected clusters with nothing tying them together. Types whose shape makes a high count expected — and which would otherwise dominate this list — are excluded before this row is raised, so this is a genuine split candidate rather than a metric reading. It is still a shape, not a defect: confirm the groups match responsibilities you can name before splitting.
Low cohesion: SubWorkflowExecutionActor (LCOM4 6) engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActor.scala:32 — SubWorkflowExecutionActor's methods fall into 6 groups that share no field and call none of each other, against a bar of more than 3 for this run (LCOM4, configurable — your repository's bar is the one quoted here). Each group is a set of methods reachable from one another through shared fields or direct calls, so 6 groups means the type has that many internally-connected clusters with nothing tying them together. Types whose shape makes a high count expected — and which would otherwise dominate this list — are excluded before this row is raised, so this is a genuine split candidate rather than a metric reading. It is still a shape, not a defect: confirm the groups match responsibilities you can name before splitting.
Low cohesion: CloudNioFileSystemProvider (LCOM4 4) cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioFileSystemProvider.scala:18 — CloudNioFileSystemProvider's methods fall into 4 groups that share no field and call none of each other, against a bar of more than 3 for this run (LCOM4, configurable — your repository's bar is the one quoted here). Each group is a set of methods reachable from one another through shared fields or direct calls, so 4 groups means the type has that many internally-connected clusters with nothing tying them together. Types whose shape makes a high count expected — and which would otherwise dominate this list — are excluded before this row is raised, so this is a genuine split candidate rather than a metric reading. It is still a shape, not a defect: confirm the groups match responsibilities you can name before splitting.
Low cohesion: CallCacheHashingJobActor (LCOM4 4) engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheHashingJobActor.scala:34 — CallCacheHashingJobActor's methods fall into 4 groups that share no field and call none of each other, against a bar of more than 3 for this run (LCOM4, configurable — your repository's bar is the one quoted here). Each group is a set of methods reachable from one another through shared fields or direct calls, so 4 groups means the type has that many internally-connected clusters with nothing tying them together. Types whose shape makes a high count expected — and which would otherwise dominate this list — are excluded before this row is raised, so this is a genuine split candidate rather than a metric reading. It is still a shape, not a defect: confirm the groups match responsibilities you can name before splitting.
Low cohesion: EngineJobExecutionActor (LCOM4 4) engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala:64 — EngineJobExecutionActor's methods fall into 4 groups that share no field and call none of each other, against a bar of more than 3 for this run (LCOM4, configurable — your repository's bar is the one quoted here). Each group is a set of methods reachable from one another through shared fields or direct calls, so 4 groups means the type has that many internally-connected clusters with nothing tying them together. Types whose shape makes a high count expected — and which would otherwise dominate this list — are excluded before this row is raised, so this is a genuine split candidate rather than a metric reading. It is still a shape, not a defect: confirm the groups match responsibilities you can name before splitting.

D4 · Code Duplication · Duplicated block (11 lines × 2) · ×5

Duplicated block (11 lines × 2) backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala:1111 — backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala:1111-1121 | supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala:1187-1197 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. Read the line range as the matched WINDOW rather than a finished unit: at `backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala:1111` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (11 lines × 2) backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala:92 — backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala:92-102 | backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala:140-150 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (11 lines × 2) wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/TaskDefinitionElementToWomTaskDefinition.scala:135 — wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/TaskDefinitionElementToWomTaskDefinition.scala:135-145 | wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/WorkflowDefinitionElementToWomWorkflowDefinition.scala:199-209 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once. Read the line range as the matched WINDOW rather than a finished unit: at `wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/TaskDefinitionElementToWomTaskDefinition.scala:135` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (11 lines × 2) wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala:49 — wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala:49-59 | wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/ScatterElementToGraphNode.scala:79-89 — before extracting anything, compare `wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala` and `wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/ScatterElementToGraphNode.scala` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 37 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place. Read the line range as the matched WINDOW rather than a finished unit: at `wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala:49` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (11 lines × 2) scripts/metadata_comparison/metadata_comparison/lib/operations_digesters.py:192 — scripts/metadata_comparison/metadata_comparison/lib/operations_digesters.py:192-202 | scripts/metadata_comparison/metadata_comparison/lib/operations_digesters.py:262-272 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.

D4 · Code Duplication · Duplicated block (7 lines × 2) · ×5

Duplicated block (7 lines × 2) cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/GoogleConfiguration.scala:107 — cloudSupport/src/main/scala/cromwell/cloudsupport/aws/AwsConfiguration.scala:152-158 | cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/GoogleConfiguration.scala:107-113 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. Each matched range is the entire body of the declaration above it, so the region is already a complete unit: move that whole declaration to the shared location and have each site call it, rather than lifting the lines out of their bodies. Any `return` inside it is the body's own exit and keeps its meaning in the moved unit.
Duplicated block (7 lines × 2) cromwellApiClient/src/main/scala/cromwell/api/CromwellClient.scala:254 — cromwellApiClient/src/main/scala/cromwell/api/CromwellClient.scala:254-260 | cromwellApiClient/src/main/scala/cromwell/api/CromwellClient.scala:276-282 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `cromwellApiClient/src/main/scala/cromwell/api/CromwellClient.scala:254` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (7 lines × 2) engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala:261 — engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala:261-267 | engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala:183-189 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. Read the line range as the matched WINDOW rather than a finished unit: at `engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala:261` it runs out through the closing brace of the declaration holding it and carries on into the declaration that follows — the window is the tail of one member plus the head of the next, so no call can be substituted for those exact lines, and the smallest declaration that contains all of them is the type they sit in. The repeated unit is the member each site sits in: where those members' bodies are the same, move one whole member to the shared location and have the others delegate to it; where the copies are a run of near-identical overloads or wrappers that differ only in their signatures, the repetition IS the run — a one-line delegation has no helper inside it to lift — so generate the run from the set it enumerates, or accept it and keep each member's own documentation with it.
Duplicated block (7 lines × 2) wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/FileEvaluator.scala:84 — wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/FileEvaluator.scala:84-90 | wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/FileEvaluator.scala:108-114 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/FileEvaluator.scala:84` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (7 lines × 2) wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala:138 — wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala:138-145 | wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/ValueEvaluator.scala:111-117 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once. Read the line range as the matched WINDOW rather than a finished unit: at `wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala:138` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.

D4 · Code Duplication · Duplicated block (8 lines × 2) · ×4

Duplicated block (8 lines × 2) engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala:225 — engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala:225-232 | engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala:146-153 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. Read the line range as the matched WINDOW rather than a finished unit: at `engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala:225` it runs out through the closing brace of the declaration holding it and carries on into the declaration that follows — the window is the tail of one member plus the head of the next, so no call can be substituted for those exact lines, and the smallest declaration that contains all of them is the type they sit in. The repeated unit is the member each site sits in: where those members' bodies are the same, move one whole member to the shared location and have the others delegate to it; where the copies are a run of near-identical overloads or wrappers that differ only in their signatures, the repetition IS the run — a one-line delegation has no helper inside it to lift — so generate the run from the set it enumerates, or accept it and keep each member's own documentation with it.
Duplicated block (8 lines × 2) supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/BatchInstrumentation.scala:41 — supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/BatchInstrumentation.scala:41-48 | supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/BatchInstrumentation.scala:50-57 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (8 lines × 2) wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/BiscayneAstNodeToKvPair.scala:11 — wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/BiscayneAstNodeToKvPair.scala:11-18 | wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/CascadesAstNodeToKvPair.scala:11-18 — before extracting anything, compare `wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/BiscayneAstNodeToKvPair.scala` and `wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/CascadesAstNodeToKvPair.scala` as WHOLE FILES: 88% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 1 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. The two sit in different directories, so one cannot simply be deleted in favour of the other while both are reached separately: hoist the shared part into a location both already depend on and have each file call it, and retire whichever file turns out to have no caller of its own left. Extracting one helper per block leaves the fork in place. Read the line range as the matched WINDOW rather than a finished unit: at `wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/BiscayneAstNodeToKvPair.scala:11` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (8 lines × 2) wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala:73 — wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala:73-80 | wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala:73-80 — before extracting anything, compare `wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala` and `wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala` as WHOLE FILES: 98% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 1 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. The two sit in different directories, so one cannot simply be deleted in favour of the other while both are reached separately: hoist the shared part into a location both already depend on and have each file call it, and retire whichever file turns out to have no caller of its own left. Extracting one helper per block leaves the fork in place.

D29 · Static Analysis (SAST) · REDACTED

REDACTED
REDACTED

D35 · Change Coupling · Change coupling · ×2

Change coupling: Dependencies.scala ↔ Merging.scala project/Dependencies.scala — `project/Dependencies.scala` and `project/Merging.scala` change together 90% of the time (9 of the 10 commits that touched whichever of the two files changed less often, counting a file under its earlier names as well — a repo-wide or module-wide sweep is evidence about the sweep rather than about any pair inside it and is left out of BOTH sides of this ratio, while a dependency bump, a formatter/rename sweep, or a commit whose edit to one of the two files was a tool directive such as //go:generate or whitespace only is left out of the shared count ONLY, so the two sides are not taken over identical commit sets). They sit in the same directory, and in this ecosystem sibling files there normally share one namespace/package — so a direct reference between them needs no import and this pass cannot see whether one exists. Read the pair before acting: if one file only DECLARES what the other consumes (a constants/types file beside its user), the co-change is definitional and the question is whether the split earns its keep; if they duplicate structure, extract the common part into a shared function or type they both call; if neither holds, the coupling is hidden and worth breaking. You can check this without leaving the row: of the 9 shared commits counted here, the most recent 3 are `82d90116` CTM-563 Upgrade Jackson, remove Bard et al. (#7894); `8cb78dfa` WX-1763 Update to jakarta Bard client (#7475); `23e39191` WX-1122 Use legacy AppInsights to get better control over logging (#7… — run `git show` on any of them.
Change coupling: GcpBatchAsyncBackendJobExecutionActor.scala ↔ BatchRequestExecutor.scala supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala — `supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala` and `supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/request/BatchRequestExecutor.scala` change together 60% of the time (9 of the 15 commits that touched whichever of the two files changed less often, counting a file under its earlier names as well — a repo-wide or module-wide sweep is evidence about the sweep rather than about any pair inside it and is left out of BOTH sides of this ratio, while a dependency bump, a formatter/rename sweep, or a commit whose edit to one of the two files was a tool directive such as //go:generate or whitespace only is left out of the shared count ONLY, so the two sides are not taken over identical commit sets) with no explicit dependency — the edge is real but nothing declares it. Read the pair before acting: if one registers itself into the other through a hook or an initialiser, the missing dependency is DELIBERATE — the registration is the link, and it is meant not to be an import — and the thing to add is a comment on each side naming the other, not a merge; if they simply belong together, co-locate them; if neither holds, the coupling is hidden and worth breaking. You can check this without leaving the row: of the 9 shared commits counted here, the most recent 3 are `9f610ee3` CTM-503 Fix confusing Batch task error message (#7877); `ae5763e7` [AN-695] Don't submit duplicate Batch jobs upon restart (#7782); `a1bee937` AN-428 Automatically resubmit some types of Batch failures (#7706) — run `git show` on any of them.

D4 · Code Duplication · Edited copy of a member (19 corresponding lines) · ×2

Edited copy of a member (19 corresponding lines) wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlExpression.scala:260 — wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlExpression.scala:260-293 | wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/WdlStandardLibraryFunctions.scala:398-460 — These two members are one piece of code written twice and then edited apart: 19 consecutive lines correspond almost exactly, broken only by small local edits. Most of that correspondence is NOT reported as duplicated blocks below — the edits cut it into fragments and only the largest of them clear the block floor, so the rows below understate it. The repair is at the members' grain — factor the shared implementation into one the two call with their differences as parameters or as an injected step, or, where the difference is systematic (an extra return value, one transport against another), generate one from the other. Left alone, the next edit has to be made twice and the two will drift further apart.
Edited copy of a member (19 corresponding lines) scripts/metadata_comparison/metadata_comparison/lib/operations_digesters.py:192 — scripts/metadata_comparison/metadata_comparison/lib/operations_digesters.py:192-211 | scripts/metadata_comparison/metadata_comparison/lib/operations_digesters.py:262-280 — These two members are one piece of code written twice and then edited apart: 19 consecutive lines correspond almost exactly, broken only by small local edits. Most of that correspondence is NOT reported as duplicated blocks below — the edits cut it into fragments and only the largest of them clear the block floor, so the rows below understate it. The repair is at the members' grain — factor the shared implementation into one the two call with their differences as parameters or as an injected step, or, where the difference is systematic (an extra return value, one transport against another), generate one from the other. Left alone, the next edit has to be made twice and the two will drift further apart.

D4 · Code Duplication · Duplicated block (13–14 lines × 2) · ×2

Duplicated block (13–14 lines × 2) backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala:1535 — backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala:1535-1547 | supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala:973-986 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. Read the line range as the matched WINDOW rather than a finished unit: at `backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala:1535` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (13–14 lines × 2) wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala:75 — wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala:75-87 | wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/ScatterElementToGraphNode.scala:106-119 — before extracting anything, compare `wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala` and `wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/ScatterElementToGraphNode.scala` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 37 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place. Read the line range as the matched WINDOW rather than a finished unit: at `wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala:75` it runs out through the closing brace of the declaration holding it — the window is that declaration's tail, not a fragment that begins part-way through something, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.

D4 · Code Duplication · Duplicated block (12 lines × 2) · ×2

Duplicated block (12 lines × 2) wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomCallNodeMaker.scala:108 — wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomCallNodeMaker.scala:108-119 | wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/CallElementToGraphNode.scala:145-156 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. Read the line range as the matched WINDOW rather than a finished unit: at `wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomCallNodeMaker.scala:108` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (12 lines × 2) wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala:60 — wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala:60-71 | wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/ScatterElementToGraphNode.scala:90-101 — before extracting anything, compare `wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala` and `wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/ScatterElementToGraphNode.scala` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 37 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together — extracting one helper per block leaves the fork in place. Read the line range as the matched WINDOW rather than a finished unit: at `wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala:60` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.

D4 · Code Duplication · Duplicated block (10 lines × 2) · ×2

Duplicated block (10 lines × 2) engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala:250 — engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala:250-259 | engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala:172-181 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. Read the line range as the matched WINDOW rather than a finished unit: at `engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala:250` it runs out through the closing brace of the declaration holding it and carries on into the declaration that follows — the window is the tail of one member plus the head of the next, so no call can be substituted for those exact lines, and the smallest declaration that contains all of them is the type they sit in. The repeated unit is the member each site sits in: where those members' bodies are the same, move one whole member to the shared location and have the others delegate to it; where the copies are a run of near-identical overloads or wrappers that differ only in their signatures, the repetition IS the run — a one-line delegation has no helper inside it to lift — so generate the run from the set it enumerates, or accept it and keep each member's own documentation with it.
Duplicated block (10 lines × 2) supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala:720 — supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala:480-489 | supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala:720-730 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. Read the line range as the matched WINDOW rather than a finished unit: at `supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala:480` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.

D4 · Code Duplication · Duplicated block (9 lines × 2) · ×2

Duplicated block (9 lines × 2) engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala:240 — engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala:240-248 | engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala:162-170 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. Read the line range as the matched WINDOW rather than a finished unit: at `engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala:240` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (9 lines × 2) supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchBackendCacheHitCopyingActor.scala:55 — supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala:241-249 | supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchBackendCacheHitCopyingActor.scala:55-63 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. Read the line range as the matched WINDOW rather than a finished unit: at `supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala:241` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.

D1 · Cyclomatic Complexity · ValueEvaluator.evaluate (cyclomatic 85) · ×1

ValueEvaluator.evaluate (cyclomatic 85) wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/ValueEvaluator.scala:51 — ValueEvaluator.evaluate has cyclomatic complexity 85 (threshold 15). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline.

D1 · Cyclomatic Complexity · TypeEvaluator.evaluate (cyclomatic 84) · ×1

TypeEvaluator.evaluate (cyclomatic 84) wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala:20 — TypeEvaluator.evaluate has cyclomatic complexity 84 (threshold 15). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline.

D1 · Cyclomatic Complexity · WdlNamespace.apply (cyclomatic 54) · ×1

WdlNamespace.apply (cyclomatic 54) wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlNamespace.scala:198 — WdlNamespace.apply has cyclomatic complexity 54 (threshold 15). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Where every arm is uniform — the same kind of value, with no behaviour of its own — a table keyed by the case is the shorter form; wherever the arms carry different data or different behaviour, keep them as cases, because collapsing those trades an explicit, reviewable set of cases for nothing.

D1 · Cyclomatic Complexity · CallElementToGraphNode.convert (cyclomatic 36) · ×1

CallElementToGraphNode.convert (cyclomatic 36) wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/CallElementToGraphNode.scala:31 — CallElementToGraphNode.convert has cyclomatic complexity 36 (threshold 15). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Where every arm is uniform — the same kind of value, with no behaviour of its own — a table keyed by the case is the shorter form; wherever the arms carry different data or different behaviour, keep them as cases, because collapsing those trades an explicit, reviewable set of cases for nothing.

D1 · Cyclomatic Complexity · FileEvaluator.evaluateRecursive (cyclomatic 35) · ×1

FileEvaluator.evaluateRecursive (cyclomatic 35) wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/FileEvaluator.scala:71 — FileEvaluator.evaluateRecursive has cyclomatic complexity 35 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function so the top-level body reads as a short sequence of named decisions.

D1 · Cyclomatic Complexity · EnhancedAstNode.womValue (cyclomatic 27) · ×1

EnhancedAstNode.womValue (cyclomatic 27) wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala:179 — EnhancedAstNode.womValue has cyclomatic complexity 27 (threshold 15). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Where every arm is uniform — the same kind of value, with no behaviour of its own — a table keyed by the case is the shorter form; wherever the arms carry different data or different behaviour, keep them as cases, because collapsing those trades an explicit, reviewable set of cases for nothing.

D1 · Cyclomatic Complexity · AstNodeToExpressionElement.convert (cyclomatic 27) · ×1

AstNodeToExpressionElement.convert (cyclomatic 27) wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToExpressionElement.scala:26 — AstNodeToExpressionElement.convert has cyclomatic complexity 27 (threshold 15). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Where every arm is uniform — the same kind of value, with no behaviour of its own — a table keyed by the case is the shorter form; wherever the arms carry different data or different behaviour, keep them as cases, because collapsing those trades an explicit, reviewable set of cases for nothing.

D1 · Cyclomatic Complexity · WomArrayType.coercion (cyclomatic 26) · ×1

WomArrayType.coercion (cyclomatic 26) wom/src/main/scala/wom/types/WomArrayType.scala:24 — WomArrayType.coercion has cyclomatic complexity 26 (threshold 15). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Where every arm is uniform — the same kind of value, with no behaviour of its own — a table keyed by the case is the shorter form; wherever the arms carry different data or different behaviour, keep them as cases, because collapsing those trades an explicit, reviewable set of cases for nothing.

D1 · Cyclomatic Complexity · StandardAsyncExecutionActor.handleExecutionResult (cyclomatic 25) · ×1

StandardAsyncExecutionActor.handleExecutionResult (cyclomatic 25) backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala:1426 — StandardAsyncExecutionActor.handleExecutionResult has cyclomatic complexity 25 (threshold 15). To reduce it, separate the branches: extract each independent case into its own named function so the top-level body reads as a short sequence of named decisions.

D1 · Cyclomatic Complexity · PartialWorkflowSources.fromSubmitRoute (cyclomatic 24) · ×1

PartialWorkflowSources.fromSubmitRoute (cyclomatic 24) engine/src/main/scala/cromwell/webservice/PartialWorkflowSources.scala:80 — PartialWorkflowSources.fromSubmitRoute has cyclomatic complexity 24 (threshold 15). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Where every arm is uniform — the same kind of value, with no behaviour of its own — a table keyed by the case is the shorter form; wherever the arms carry different data or different behaviour, keep them as cases, because collapsing those trades an explicit, reviewable set of cases for nothing.

D1 · Cyclomatic Complexity · Scope.lookupFunction (cyclomatic 21) · ×1

Scope.lookupFunction (cyclomatic 21) wdl/model/draft2/src/main/scala/wdl/draft2/model/Scope.scala:234 — Scope.lookupFunction has cyclomatic complexity 21 (threshold 15). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Where every arm is uniform — the same kind of value, with no behaviour of its own — a table keyed by the case is the shorter form; wherever the arms carry different data or different behaviour, keep them as cases, because collapsing those trades an explicit, reviewable set of cases for nothing.

D1 · Cyclomatic Complexity · WdlDraft2WomCallNodeMaker.toWomCallNode (cyclomatic 21) · ×1

WdlDraft2WomCallNodeMaker.toWomCallNode (cyclomatic 21) wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomCallNodeMaker.scala:33 — WdlDraft2WomCallNodeMaker.toWomCallNode has cyclomatic complexity 21 (threshold 15). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Where every arm is uniform — the same kind of value, with no behaviour of its own — a table keyed by the case is the shorter form; wherever the arms carry different data or different behaviour, keep them as cases, because collapsing those trades an explicit, reviewable set of cases for nothing.

D1 · Cyclomatic Complexity · GcpBatchConfigurationAttributes.apply (cyclomatic 20) · ×1

GcpBatchConfigurationAttributes.apply (cyclomatic 20) supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationAttributes.scala:138 — GcpBatchConfigurationAttributes.apply has cyclomatic complexity 20 (threshold 15). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Where every arm is uniform — the same kind of value, with no behaviour of its own — a table keyed by the case is the shorter form; wherever the arms carry different data or different behaviour, keep them as cases, because collapsing those trades an explicit, reviewable set of cases for nothing.

D1 · Cyclomatic Complexity · EnhancedAstNode.womType (cyclomatic 19) · ×1

EnhancedAstNode.womType (cyclomatic 19) wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala:125 — EnhancedAstNode.womType has cyclomatic complexity 19 (threshold 15). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Where every arm is uniform — the same kind of value, with no behaviour of its own — a table keyed by the case is the shorter form; wherever the arms carry different data or different behaviour, keep them as cases, because collapsing those trades an explicit, reviewable set of cases for nothing.

D1 · Cyclomatic Complexity · WdlCall.lookupFunction (cyclomatic 18) · ×1

WdlCall.lookupFunction (cyclomatic 18) wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlCall.scala:143 — WdlCall.lookupFunction has cyclomatic complexity 18 (threshold 15). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline.

D1 · Cyclomatic Complexity · WdlNamespace.validateCallInputSection (cyclomatic 18) · ×1

WdlNamespace.validateCallInputSection (cyclomatic 18) wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlNamespace.scala:600 — WdlNamespace.validateCallInputSection has cyclomatic complexity 18 (threshold 15). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Where every arm is uniform — the same kind of value, with no behaviour of its own — a table keyed by the case is the shorter form; wherever the arms carry different data or different behaviour, keep them as cases, because collapsing those trades an explicit, reviewable set of cases for nothing.

D1 · Cyclomatic Complexity · WorkflowExecutionActor.startRunnableNodes (cyclomatic 17) · ×1

WorkflowExecutionActor.startRunnableNodes (cyclomatic 17) engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActor.scala:620 — WorkflowExecutionActor.startRunnableNodes has cyclomatic complexity 17 (threshold 15). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Where every arm is uniform — the same kind of value, with no behaviour of its own — a table keyed by the case is the shorter form; wherever the arms carry different data or different behaviour, keep them as cases, because collapsing those trades an explicit, reviewable set of cases for nothing.

D1 · Cyclomatic Complexity · CromwellApiService.submitRequest (cyclomatic 17) · ×1

CromwellApiService.submitRequest (cyclomatic 17) engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala:217 — CromwellApiService.submitRequest has cyclomatic complexity 17 (threshold 15). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Where every arm is uniform — the same kind of value, with no behaviour of its own — a table keyed by the case is the shorter form; wherever the arms carry different data or different behaviour, keep them as cases, because collapsing those trades an explicit, reviewable set of cases for nothing.

D1 · Cyclomatic Complexity · WesRouteSupport.wesSubmitRequest (cyclomatic 17) · ×1

WesRouteSupport.wesSubmitRequest (cyclomatic 17) engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala:139 — WesRouteSupport.wesSubmitRequest has cyclomatic complexity 17 (threshold 15). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Where every arm is uniform — the same kind of value, with no behaviour of its own — a table keyed by the case is the shorter form; wherever the arms carry different data or different behaviour, keep them as cases, because collapsing those trades an explicit, reviewable set of cases for nothing.

D1 · Cyclomatic Complexity · OutputEvaluator.evaluateOutputs (cyclomatic 16) · ×1

OutputEvaluator.evaluateOutputs (cyclomatic 16) backend/src/main/scala/cromwell/backend/OutputEvaluator.scala:27 — OutputEvaluator.evaluateOutputs has cyclomatic complexity 16 (threshold 15). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Where every arm is uniform — the same kind of value, with no behaviour of its own — a table keyed by the case is the shorter form; wherever the arms carry different data or different behaviour, keep them as cases, because collapsing those trades an explicit, reviewable set of cases for nothing.

D1 · Cyclomatic Complexity · WomValueBuilder.toWomValue (cyclomatic 16) · ×1

WomValueBuilder.toWomValue (cyclomatic 16) core/src/main/scala/cromwell/core/simpleton/WomValueBuilder.scala:90 — WomValueBuilder.toWomValue has cyclomatic complexity 16 (threshold 15). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Where every arm is uniform — the same kind of value, with no behaviour of its own — a table keyed by the case is the shorter form; wherever the arms carry different data or different behaviour, keep them as cases, because collapsing those trades an explicit, reviewable set of cases for nothing.

D1 · Cyclomatic Complexity · ParameterCommandPart.instantiate (cyclomatic 16) · ×1

ParameterCommandPart.instantiate (cyclomatic 16) wdl/model/draft2/src/main/scala/wdl/draft2/model/command/ParameterCommandPart.scala:43 — ParameterCommandPart.instantiate has cyclomatic complexity 16 (threshold 15). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Where every arm is uniform — the same kind of value, with no behaviour of its own — a table keyed by the case is the shorter form; wherever the arms carry different data or different behaviour, keep them as cases, because collapsing those trades an explicit, reviewable set of cases for nothing.

D2 · Cognitive Complexity · ValueEvaluator.evaluate (cognitive 157) · ×1

ValueEvaluator.evaluate (cognitive 157) wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/ValueEvaluator.scala:51 — ValueEvaluator.evaluate has cognitive complexity 157 (threshold 15). Drivers by points: loops 28 (95 pts), match/switch 14 (41 pts), if/else 17 (21 pts) (nesting depth added 98). The drivers above price the dispatch low by construction — a dispatch is charged once however many cases it lists, while each branch inside an arm is charged in full — so most of this count is what the case bodies hold, and the arms are where it can be reduced. To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Keep every case explicit, and make the behaviour for cases you do not list a deliberate choice rather than an accident.

D2 · Cognitive Complexity · TypeEvaluator.evaluate (cognitive 147) · ×1

TypeEvaluator.evaluate (cognitive 147) wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala:20 — TypeEvaluator.evaluate has cognitive complexity 147 (threshold 15). Drivers by points: loops 32 (109 pts), match/switch 12 (32 pts), if/else 6 (nesting depth added 97). The drivers above price the dispatch low by construction — a dispatch is charged once however many cases it lists, while each branch inside an arm is charged in full — so most of this count is what the case bodies hold, and the arms are where it can be reduced. To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Keep every case explicit, and make the behaviour for cases you do not list a deliberate choice rather than an accident.

D2 · Cognitive Complexity · FileEvaluator.evaluateRecursive (cognitive 79) · ×1

FileEvaluator.evaluateRecursive (cognitive 79) wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/FileEvaluator.scala:71 — FileEvaluator.evaluateRecursive has cognitive complexity 79 (threshold 15). Drivers by points: loops 9 (32 pts), match/switch 13 (31 pts), if/else 15 (16 pts) (nesting depth added 42). The drivers above price the dispatch low by construction — a dispatch is charged once however many cases it lists, while each branch inside an arm is charged in full — so most of this count is what the case bodies hold, and the arms are where it can be reduced. To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Keep every case explicit, and make the behaviour for cases you do not list a deliberate choice rather than an accident.

D2 · Cognitive Complexity · WdlNamespace.apply (cognitive 61) · ×1

WdlNamespace.apply (cognitive 61) wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlNamespace.scala:198 — WdlNamespace.apply has cognitive complexity 61 (threshold 15). Drivers by points: loops 17 (28 pts), match/switch 20 (26 pts), if/else 6, boolean chains 1 (nesting depth added 17). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline.

D2 · Cognitive Complexity · MaterializeWorkflowDescriptorActor.buildWorkflowDescriptor (cognitive 53) · ×1

MaterializeWorkflowDescriptorActor.buildWorkflowDescriptor (cognitive 53) engine/src/main/scala/cromwell/engine/workflow/lifecycle/materialization/MaterializeWorkflowDescriptorActor.scala:304 — MaterializeWorkflowDescriptorActor.buildWorkflowDescriptor has cognitive complexity 53 (threshold 15). Drivers by points: loops 8 (36 pts), match/switch 2 (10 pts), if/else 3 (7 pts) (nesting depth added 40). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline.

D2 · Cognitive Complexity · CallElementToGraphNode.convert (cognitive 52) · ×1

CallElementToGraphNode.convert (cognitive 52) wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/CallElementToGraphNode.scala:31 — CallElementToGraphNode.convert has cognitive complexity 52 (threshold 15). Drivers by points: if/else 15 (22 pts), match/switch 10 (17 pts), loops 5 (9 pts), boolean chains 4 (nesting depth added 18). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body.

D2 · Cognitive Complexity · GcpBatchAsyncBackendJobExecutionActor.executeAsync (cognitive 46) · ×1

GcpBatchAsyncBackendJobExecutionActor.executeAsync (cognitive 46) supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala:928 — GcpBatchAsyncBackendJobExecutionActor.executeAsync has cognitive complexity 46 (threshold 15). Drivers by points: loops 9 (45 pts), match/switch 1 (nesting depth added 36). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline.

D2 · Cognitive Complexity · CallCacheDiffActor.extractCallMetadata (cognitive 45) · ×1

CallCacheDiffActor.extractCallMetadata (cognitive 45) engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheDiffActor.scala:170 — CallCacheDiffActor.extractCallMetadata has cognitive complexity 45 (threshold 15). Drivers by points: loops 9 (45 pts) (nesting depth added 36). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline.

D2 · Cognitive Complexity · ArchiveMetadataConfig.parseConfig (cognitive 45) · ×1

ArchiveMetadataConfig.parseConfig (cognitive 45) services/src/main/scala/cromwell/services/metadata/impl/archiver/ArchiveMetadataConfig.scala:28 — ArchiveMetadataConfig.parseConfig has cognitive complexity 45 (threshold 15). Drivers by points: loops 9 (45 pts) (nesting depth added 36). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline.

D2 · Cognitive Complexity · WdlCall.lookupFunction (cognitive 34) · ×1

WdlCall.lookupFunction (cognitive 34) wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlCall.scala:143 — WdlCall.lookupFunction has cognitive complexity 34 (threshold 15). Drivers by points: loops 12 (27 pts), match/switch 4, if/else 3 (nesting depth added 15). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline.

D2 · Cognitive Complexity · StandardAsyncExecutionActor.handleExecutionResult (cognitive 33) · ×1

StandardAsyncExecutionActor.handleExecutionResult (cognitive 33) backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala:1426 — StandardAsyncExecutionActor.handleExecutionResult has cognitive complexity 33 (threshold 15). Drivers by points: if/else 10 (11 pts), match/switch 5 (10 pts), loops 5 (9 pts), boolean chains 3 (nesting depth added 10). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body.

D2 · Cognitive Complexity · comparer.error_checks (cognitive 29) · ×1

comparer.error_checks (cognitive 29) scripts/metadata_comparison/metadata_comparison/comparer.py:321 — comparer.error_checks has cognitive complexity 29 (threshold 15). Drivers by points: if/else 11 (22 pts), loops 4 (7 pts) (nesting depth added 14). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body.

D2 · Cognitive Complexity · MetadataSlickDatabase.summarizeDecreasing (cognitive 26) · ×1

MetadataSlickDatabase.summarizeDecreasing (cognitive 26) database/sql/src/main/scala/cromwell/database/slick/MetadataSlickDatabase.scala:318 — MetadataSlickDatabase.summarizeDecreasing has cognitive complexity 26 (threshold 15). Drivers by points: loops 6 (21 pts), match/switch 2 (5 pts) (nesting depth added 18). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline.

D2 · Cognitive Complexity · MetadataBuilderActor.computeCost (cognitive 24) · ×1

MetadataBuilderActor.computeCost (cognitive 24) services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataBuilderActor.scala:355 — MetadataBuilderActor.computeCost has cognitive complexity 24 (threshold 15). Drivers by points: loops 3 (12 pts), if/else 5 (8 pts), match/switch 2 (4 pts) (nesting depth added 14). The drivers above price the dispatch low by construction — a dispatch is charged once however many cases it lists, while each branch inside an arm is charged in full — so most of this count is what the case bodies hold, and the arms are where it can be reduced. To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Keep every case explicit, and make the behaviour for cases you do not list a deliberate choice rather than an accident.

D2 · Cognitive Complexity · WdlDraft2LanguageFactory.validateNamespace (cognitive 23) · ×1

WdlDraft2LanguageFactory.validateNamespace (cognitive 23) languageFactories/wdl-draft2/src/main/scala/languages/wdl/draft2/WdlDraft2LanguageFactory.scala:45 — WdlDraft2LanguageFactory.validateNamespace has cognitive complexity 23 (threshold 15). Drivers by points: loops 6 (21 pts), match/switch 2 (nesting depth added 15). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline.

D2 · Cognitive Complexity · CostCatalogKey.apply (cognitive 21) · ×1

CostCatalogKey.apply (cognitive 21) services/src/main/scala/cromwell/services/cost/GcpCostCatalogService.scala:43 — CostCatalogKey.apply has cognitive complexity 21 (threshold 15). Drivers by points: loops 6 (21 pts) (nesting depth added 15). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline. This shape REPEATS in the file: one other method here (GcpCostCatalogService.calculateVmCostPerHour) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.

D2 · Cognitive Complexity · GcpCostCatalogService.calculateVmCostPerHour (cognitive 21) · ×1

GcpCostCatalogService.calculateVmCostPerHour (cognitive 21) services/src/main/scala/cromwell/services/cost/GcpCostCatalogService.scala:215 — GcpCostCatalogService.calculateVmCostPerHour has cognitive complexity 21 (threshold 15). Drivers by points: loops 6 (21 pts) (nesting depth added 15). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline. This shape REPEATS in the file: one other method here (CostCatalogKey.apply) has the same decision points, in the same order, at the same nesting depths — so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared.

D2 · Cognitive Complexity · MetadataBuilderActor.buildCostAndStop (cognitive 21) · ×1

MetadataBuilderActor.buildCostAndStop (cognitive 21) services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataBuilderActor.scala:624 — MetadataBuilderActor.buildCostAndStop has cognitive complexity 21 (threshold 15). Drivers by points: loops 5 (15 pts), match/switch 4, if/else 2 (nesting depth added 10). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline.

D2 · Cognitive Complexity · JobStoreWriterActor.process (cognitive 20) · ×1

JobStoreWriterActor.process (cognitive 20) engine/src/main/scala/cromwell/jobstore/JobStoreWriterActor.scala:27 — JobStoreWriterActor.process has cognitive complexity 20 (threshold 15). Drivers by points: match/switch 6 (13 pts), loops 2 (5 pts), if/else 2 (nesting depth added 10). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Keep every case explicit, and make the behaviour for cases you do not list a deliberate choice rather than an accident.

D2 · Cognitive Complexity · AstNodeToExpressionElement.convert (cognitive 19) · ×1

AstNodeToExpressionElement.convert (cognitive 19) wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToExpressionElement.scala:26 — AstNodeToExpressionElement.convert has cognitive complexity 19 (threshold 15). Drivers by points: loops 4 (9 pts), match/switch 4 (7 pts), if/else 2, boolean chains 1 (nesting depth added 8). The drivers above price the dispatch low by construction — a dispatch is charged once however many cases it lists, while each branch inside an arm is charged in full — so most of this count is what the case bodies hold, and the arms are where it can be reduced. To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Keep every case explicit, and make the behaviour for cases you do not list a deliberate choice rather than an accident.

D2 · Cognitive Complexity · EnhancedAstNode.womValue (cognitive 18) · ×1

EnhancedAstNode.womValue (cognitive 18) wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala:179 — EnhancedAstNode.womValue has cognitive complexity 18 (threshold 15). Drivers by points: boolean chains 11, if/else 4, match/switch 2 (3 pts) (nesting depth added 1). To reduce it, name the conditions: bind each compound test to a well-named local or a small predicate function, so the body reads as a sequence of named decisions rather than a chain of operators.

D2 · Cognitive Complexity · WdlDraft2WomCallNodeMaker.toWomCallNode (cognitive 18) · ×1

WdlDraft2WomCallNodeMaker.toWomCallNode (cognitive 18) wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomCallNodeMaker.scala:33 — WdlDraft2WomCallNodeMaker.toWomCallNode has cognitive complexity 18 (threshold 15). Drivers by points: match/switch 8 (9 pts), loops 4 (6 pts), if/else 2, boolean chains 1 (nesting depth added 3). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Keep every case explicit, and make the behaviour for cases you do not list a deliberate choice rather than an accident.

D2 · Cognitive Complexity · ReadMetadataRegulatorActor.receive (cognitive 17) · ×1

ReadMetadataRegulatorActor.receive (cognitive 17) services/src/main/scala/cromwell/services/metadata/impl/ReadMetadataRegulatorActor.scala:38 — ReadMetadataRegulatorActor.receive has cognitive complexity 17 (threshold 15). Drivers by points: if/else 5 (12 pts), match/switch 3 (5 pts) (nesting depth added 9). The drivers above price the dispatch low by construction — a dispatch is charged once however many cases it lists, while each branch inside an arm is charged in full — so most of this count is what the case bodies hold, and the arms are where it can be reduced. To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Keep every case explicit, and make the behaviour for cases you do not list a deliberate choice rather than an accident.

D2 · Cognitive Complexity · ArchiveMetadataSchedulerActor.streamMetadataToGcs (cognitive 17) · ×1

ArchiveMetadataSchedulerActor.streamMetadataToGcs (cognitive 17) services/src/main/scala/cromwell/services/metadata/impl/archiver/ArchiveMetadataSchedulerActor.scala:257 — ArchiveMetadataSchedulerActor.streamMetadataToGcs has cognitive complexity 17 (threshold 15). Drivers by points: loops 4 (10 pts), if/else 4 (7 pts) (nesting depth added 9). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline.

D2 · Cognitive Complexity · GcpBatchAsyncBackendJobExecutionActor.createBatchParameters (cognitive 17) · ×1

GcpBatchAsyncBackendJobExecutionActor.createBatchParameters (cognitive 17) supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala:600 — GcpBatchAsyncBackendJobExecutionActor.createBatchParameters has cognitive complexity 17 (threshold 15). Drivers by points: match/switch 4 (8 pts), loops 2 (5 pts), if/else 3 (4 pts) (nesting depth added 8). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Keep every case explicit, and make the behaviour for cases you do not list a deliberate choice rather than an accident.

D2 · Cognitive Complexity · Scope.lookupFunction (cognitive 17) · ×1

Scope.lookupFunction (cognitive 17) wdl/model/draft2/src/main/scala/wdl/draft2/model/Scope.scala:234 — Scope.lookupFunction has cognitive complexity 17 (threshold 15). Drivers by points: match/switch 7 (10 pts), if/else 6, boolean chains 1 (nesting depth added 3). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Keep every case explicit, and make the behaviour for cases you do not list a deliberate choice rather than an accident.

D2 · Cognitive Complexity · UnixPath.normalize (cognitive 16) · ×1

UnixPath.normalize (cognitive 16) cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala:201 — UnixPath.normalize has cognitive complexity 16 (threshold 15). Drivers by points: if/else 7 (12 pts), match/switch 1 (2 pts), boolean chains 1, loops 1 (nesting depth added 6). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body.

D2 · Cognitive Complexity · DrsPathBuilder.maybeCreateOtherPath (cognitive 16) · ×1

DrsPathBuilder.maybeCreateOtherPath (cognitive 16) filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilder.scala:36 — DrsPathBuilder.maybeCreateOtherPath has cognitive complexity 16 (threshold 15). Drivers by points: loops 5 (15 pts), match/switch 1 (nesting depth added 10). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline.

D2 · Cognitive Complexity · ArchiveMetadataSchedulerActor.receive (cognitive 16) · ×1

ArchiveMetadataSchedulerActor.receive (cognitive 16) services/src/main/scala/cromwell/services/metadata/impl/archiver/ArchiveMetadataSchedulerActor.scala:86 — ArchiveMetadataSchedulerActor.receive has cognitive complexity 16 (threshold 15). Drivers by points: if/else 5 (13 pts), match/switch 2 (3 pts) (nesting depth added 9). The drivers above price the dispatch low by construction — a dispatch is charged once however many cases it lists, while each branch inside an arm is charged in full — so most of this count is what the case bodies hold, and the arms are where it can be reduced. To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Keep every case explicit, and make the behaviour for cases you do not list a deliberate choice rather than an accident.

D2 · Cognitive Complexity · GcpLabel.safeGoogleName (cognitive 16) · ×1

GcpLabel.safeGoogleName (cognitive 16) supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpLabel.scala:28 — GcpLabel.safeGoogleName has cognitive complexity 16 (threshold 15). Drivers by points: if/else 8 (11 pts), match/switch 2 (3 pts), boolean chains 2 (nesting depth added 4). The drivers above price the dispatch low by construction — a dispatch is charged once however many cases it lists, while each branch inside an arm is charged in full — so most of this count is what the case bodies hold, and the arms are where it can be reduced. To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Keep every case explicit, and make the behaviour for cases you do not list a deliberate choice rather than an accident.

D2 · Cognitive Complexity · WomArrayType.coercion (cognitive 16) · ×1

WomArrayType.coercion (cognitive 16) wom/src/main/scala/wom/types/WomArrayType.scala:24 — WomArrayType.coercion has cognitive complexity 16 (threshold 15). Drivers by points: boolean chains 13, match/switch 2 (3 pts) (nesting depth added 1). The drivers above price the dispatch low by construction — a dispatch is charged once however many cases it lists, while each branch inside an arm is charged in full — so most of this count is what the case bodies hold, and the arms are where it can be reduced. To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Keep every case explicit, and make the behaviour for cases you do not list a deliberate choice rather than an accident.

D36 · Supply-chain Provenance & Signing · REDACTED · ×1

REDACTED

D36 · Supply-chain Provenance & Signing · REDACTED · ×1

REDACTED

D36 · Supply-chain Provenance & Signing · REDACTED · ×1

REDACTED

D4 · Code Duplication · Near-duplicate member pair (34 shared lines) · ×1

Near-duplicate member pair (34 shared lines) engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala:217 — engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala:217-270 | engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala:139-192 — These two members are variants of one another: 34 of their lines are already reported as duplicated blocks below, spread through both bodies rather than gathered into one. Read them as a single construct written twice. The repair is at the members' grain — factor the shared pipeline into one implementation the two call with their differences as parameters or as an injected step, or, where the difference is systematic (sync against async, one transport against another), generate one from the other. Extracting the individual blocks below is not the same fix: it leaves the two bodies in place and the next edit still has to be made twice.

D4 · Code Duplication · Members sharing a duplicated core (4 members, 50+ identical tokens) · ×1

Members sharing a duplicated core (4 members, 50+ identical tokens) wom/src/main/scala/wom/expression/WomExpression.scala:38 — supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala:301-323 | supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala:75-97 | supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala:84-106 | wom/src/main/scala/wom/expression/WomExpression.scala:38-57 — These 4 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below — it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 4 times. The repair is at the members' grain — factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 4 times.

D4 · Code Duplication · Duplicated block (29–31 lines × 3) · ×1

Duplicated block (29–31 lines × 3) supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/request/AbortRequestHandler.scala:54 — supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/request/AbortRequestHandler.scala:54-82 | supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/request/GetRequestHandler.scala:33-61 | supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/request/RunRequestHandler.scala:34-64 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from all 3 call sites, so a change lands once. Read the line range as the matched WINDOW rather than a finished unit: at `supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/request/AbortRequestHandler.scala:54` it runs out through the closing brace of the declaration holding it — the window is that declaration's tail, not a fragment that begins part-way through something, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.

D4 · Code Duplication · Duplicated block (29 lines × 2) · ×1

Duplicated block (29 lines × 2) wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/wdlom2wom/package.scala:49 — wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/wdlom2wom/package.scala:49-77 | wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/wdlom2wom/package.scala:49-77 — before extracting anything, compare `wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/wdlom2wom/package.scala` and `wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/wdlom2wom/package.scala` as WHOLE FILES: 91% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 1 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. The two sit in different directories, so one cannot simply be deleted in favour of the other while both are reached separately: hoist the shared part into a location both already depend on and have each file call it, and retire whichever file turns out to have no caller of its own left. Extracting one helper per block leaves the fork in place.

D4 · Code Duplication · Duplicated block (28 lines × 2) · ×1

Duplicated block (28 lines × 2) languageFactories/wdl-biscayne/src/main/scala/languages/wdl/biscayne/WdlBiscayneLanguageFactory.scala:69 — languageFactories/wdl-biscayne/src/main/scala/languages/wdl/biscayne/WdlBiscayneLanguageFactory.scala:69-96 | languageFactories/wdl-cascades/src/main/scala/languages/wdl/cascades/WdlCascadesLanguageFactory.scala:69-96 — before extracting anything, compare `languageFactories/wdl-biscayne/src/main/scala/languages/wdl/biscayne/WdlBiscayneLanguageFactory.scala` and `languageFactories/wdl-cascades/src/main/scala/languages/wdl/cascades/WdlCascadesLanguageFactory.scala` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 49 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. The two sit in different directories, so one cannot simply be deleted in favour of the other while both are reached separately: hoist the shared part into a location both already depend on and have each file call it, and retire whichever file turns out to have no caller of its own left. Extracting one helper per block leaves the fork in place. Each matched range is the entire body of the declaration above it, so the region is already a complete unit: move that whole declaration to the shared location and have each site call it, rather than lifting the lines out of their bodies. Any `return` inside it is the body's own exit and keeps its meaning in the moved unit.

D4 · Code Duplication · Duplicated block (26 lines × 2) · ×1

Duplicated block (26 lines × 2) cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/TryWithResource.scala:10 — cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/TryWithResource.scala:10-35 | core/src/main/scala/cromwell/util/TryWithResource.scala:10-35 — before extracting anything, compare `cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/TryWithResource.scala` and `core/src/main/scala/cromwell/util/TryWithResource.scala` as WHOLE FILES: 96% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 1 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. The two sit in different directories, so one cannot simply be deleted in favour of the other while both are reached separately: hoist the shared part into a location both already depend on and have each file call it, and retire whichever file turns out to have no caller of its own left. Extracting one helper per block leaves the fork in place.

D4 · Code Duplication · Duplicated block (24–25 lines × 2) · ×1

Duplicated block (24–25 lines × 2) CromIAM/src/main/scala/cromiam/webservice/SwaggerUiHttpService.scala:45 — CromIAM/src/main/scala/cromiam/webservice/SwaggerUiHttpService.scala:45-69 | engine/src/main/scala/cromwell/webservice/SwaggerUiHttpService.scala:54-77 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice.

D4 · Code Duplication · Duplicated block (19–22 lines × 4) · ×1

Duplicated block (19–22 lines × 4) wom/src/main/scala/wom/expression/WomExpression.scala:39 — supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala:302-323 | supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala:76-97 | supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala:85-106 | wom/src/main/scala/wom/expression/WomExpression.scala:39-57 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere all 4 call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made 4 times. Each matched range is the entire body of the declaration above it, so the region is already a complete unit: move that whole declaration to the shared location and have each site call it, rather than lifting the lines out of their bodies. Any `return` inside it is the body's own exit and keeps its meaning in the moved unit.

D4 · Code Duplication · Duplicated block (20 lines × 2) · ×1

Duplicated block (20 lines × 2) services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataBuilderActor.scala:489 — services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataBuilderActor.scala:489-508 | services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataBuilderActor.scala:520-539 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataBuilderActor.scala:489` it runs out through the closing brace of the declaration holding it — the window is that declaration's tail, not a fragment that begins part-way through something, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.

D4 · Code Duplication · Duplicated block (18 lines × 2) · ×1

Duplicated block (18 lines × 2) engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActor.scala:428 — engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActor.scala:428-445 | engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActor.scala:1019-1037 — the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once. Read the line range as the matched WINDOW rather than a finished unit: at `engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActor.scala:428` it runs out through the closing brace of the declaration holding it — the window is that declaration's tail, not a fragment that begins part-way through something, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.

D4 · Code Duplication · Duplicated block (10–17 lines × 2) · ×1

Duplicated block (10–17 lines × 2) backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala:1478 — backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala:1478-1487 | supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala:862-878 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. Read the line range as the matched WINDOW rather than a finished unit: at `backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala:1478` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.

D4 · Code Duplication · Duplicated block (15–16 lines × 3) · ×1

Duplicated block (15–16 lines × 3) languageFactories/wdl-biscayne/src/main/scala/languages/wdl/biscayne/WdlBiscayneLanguageFactory.scala:44 — languageFactories/wdl-biscayne/src/main/scala/languages/wdl/biscayne/WdlBiscayneLanguageFactory.scala:44-59 | languageFactories/wdl-cascades/src/main/scala/languages/wdl/cascades/WdlCascadesLanguageFactory.scala:44-59 | languageFactories/wdl-draft3/src/main/scala/languages/wdl/draft3/WdlDraft3LanguageFactory.scala:44-58 — before extracting anything, compare `languageFactories/wdl-biscayne/src/main/scala/languages/wdl/biscayne/WdlBiscayneLanguageFactory.scala` and `languageFactories/wdl-cascades/src/main/scala/languages/wdl/cascades/WdlCascadesLanguageFactory.scala` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 49 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. The two sit in different directories, so one cannot simply be deleted in favour of the other while both are reached separately: hoist the shared part into a location both already depend on and have each file call it, and retire whichever file turns out to have no caller of its own left. Extracting one helper per block leaves the fork in place. Each matched range is the entire body of the declaration above it, so the region is already a complete unit: move that whole declaration to the shared location and have each site call it, rather than lifting the lines out of their bodies. Any `return` inside it is the body's own exit and keeps its meaning in the moved unit.

D4 · Code Duplication · Duplicated block (16 lines × 2) · ×1

Duplicated block (16 lines × 2) cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/VersionUtil.scala:64 — cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/VersionUtil.scala:64-79 | common/src/main/scala/common/util/VersionUtil.scala:64-79 — before extracting anything, compare `cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/VersionUtil.scala` and `common/src/main/scala/common/util/VersionUtil.scala` as WHOLE FILES: 96% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 1 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. The two sit in different directories, so one cannot simply be deleted in favour of the other while both are reached separately: hoist the shared part into a location both already depend on and have each file call it, and retire whichever file turns out to have no caller of its own left. Extracting one helper per block leaves the fork in place.

D4 · Code Duplication · Duplicated block (15 lines × 2) · ×1

Duplicated block (15 lines × 2) backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala:86 — backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala:86-100 | backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala:110-124 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala:86` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.

D4 · Code Duplication · Duplicated block (14 lines × 2) · ×1

Duplicated block (14 lines × 2) database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingAggregationEntryComponent.scala:88 — database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingAggregationEntryComponent.scala:88-101 | database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingAggregationEntryComponent.scala:116-129 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingAggregationEntryComponent.scala:88` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.

D4 · Code Duplication · Duplicated block (12–13 lines × 2) · ×1

Duplicated block (12–13 lines × 2) services/src/main/scala/cromwell/services/metadata/impl/MetadataDatabaseAccess.scala:264 — services/src/main/scala/cromwell/services/metadata/impl/MetadataDatabaseAccess.scala:264-275 | services/src/main/scala/cromwell/services/metadata/impl/MetadataDatabaseAccess.scala:283-295 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.

D4 · Code Duplication · Duplicated block (13 lines × 2) · ×1

Duplicated block (13 lines × 2) wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlExpression.scala:266 — wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlExpression.scala:266-278 | wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/WdlStandardLibraryFunctions.scala:402-414 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice.

D4 · Code Duplication · Duplicated block (10–11 lines × 2) · ×1

Duplicated block (10–11 lines × 2) wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/EngineFunctionEvaluators.scala:204 — wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/EngineFunctionEvaluators.scala:204-214 | wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/EngineFunctionEvaluators.scala:222-231 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/EngineFunctionEvaluators.scala:204` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.

D4 · Code Duplication · Duplicated block (9 lines × 3) · ×1

Duplicated block (9 lines × 3) backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala:92 — backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala:92-100 | backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala:116-124 | backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala:140-148 — all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites — resolving only two of them leaves the rest to drift apart the first time one is edited.

D4 · Code Duplication · Duplicated block (6–7 lines × 2) · ×1

Duplicated block (6–7 lines × 2) wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/EngineFunctionEvaluators.scala:80 — wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/EngineFunctionEvaluators.scala:80-86 | wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/EngineFunctionEvaluators.scala:92-97 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at `wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/EngineFunctionEvaluators.scala:80` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/EngineFunctionEvaluators.scala:97` calls `renameIdentifiers` and `wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/EngineFunctionEvaluators.scala:86` does not — after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live.

D4 · Code Duplication · Duplicated block (58 lines × 3) · ×1

Duplicated block (58 lines × 3) wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/parsing/WdlBiscayneSyntaxErrorFormatter.scala:10 — wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/parsing/WdlBiscayneSyntaxErrorFormatter.scala:10-67 | wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/WdlCascadesSyntaxErrorFormatter.scala:10-67 | wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/parsing/WdlDraft3SyntaxErrorFormatter.scala:9-66 — before extracting anything, compare `wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/parsing/WdlBiscayneSyntaxErrorFormatter.scala` and `wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/WdlCascadesSyntaxErrorFormatter.scala` as WHOLE FILES: 90% of the shorter file's lines also appear in the other, so this reads as one file having been copied from the other rather than as a helper waiting to be extracted. The 1 duplicated block(s) this scan matched between them are fragments of that copy, not the extent of it — treat the file pair as the unit. The two sit in different directories, so one cannot simply be deleted in favour of the other while both are reached separately: hoist the shared part into a location both already depend on and have each file call it, and retire whichever file turns out to have no caller of its own left. Extracting one helper per block leaves the fork in place.

D4 · Code Duplication · Duplicated block (5 lines × 3) · ×1

Duplicated block (5 lines × 3) languageFactories/wdl-biscayne/src/main/scala/languages/wdl/biscayne/WdlBiscayneLanguageFactory.scala:102 — languageFactories/wdl-biscayne/src/main/scala/languages/wdl/biscayne/WdlBiscayneLanguageFactory.scala:102-106 | languageFactories/wdl-cascades/src/main/scala/languages/wdl/cascades/WdlCascadesLanguageFactory.scala:102-106 | languageFactories/wdl-draft3/src/main/scala/languages/wdl/draft3/WdlDraft3LanguageFactory.scala:119-123 — before extracting anything, compare `languageFactories/wdl-biscayne/src/main/scala/languages/wdl/biscayne/WdlBiscayneLanguageFactory.scala` and `languageFactories/wdl-cascades/src/main/scala/languages/wdl/cascades/WdlCascadesLanguageFactory.scala` as WHOLE FILES: this scan already matched 3 separate duplicated blocks between them, totalling at least 49 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. The two sit in different directories, so one cannot simply be deleted in favour of the other while both are reached separately: hoist the shared part into a location both already depend on and have each file call it, and retire whichever file turns out to have no caller of its own left. Extracting one helper per block leaves the fork in place.

M1 · Documentation (README) · README may be stale · ×1

README may be stale — 122 code files changed in the last 6 months but the README was not touched — it may no longer reflect the system.

S1 · Web-Security Posture · Third-party script without Subresource Integrity · ×1

Third-party script without Subresource Integrity engine/src/main/resources/workflowTimings/workflowTimings.html:4 — `https://www.gstatic.com/charts/loader.js` is executed by this page with no Subresource Integrity. Whoever can answer that request — the CDN, anyone who compromises it, anyone on the network path — runs arbitrary script in this page's origin, with its session. The URL also names no version, so it resolves to whatever that origin serves at fetch time — the executed bytes can change with nobody touching this repository. 2 such include(s) across the repository's markup.

Minor — 20 finding(s)

D34 · Knowledge Freshness · Most significant orphaned file · ×3

Most significant orphaned file wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala — One of the orphaned files carrying the most lost knowledge — ranked by size weighted by the file's role in the codebase, the same weighting behind the score above, so core code outranks equally large plumbing. A reasonable place to start a read-through before the aggregate risk above bites.
Most significant orphaned file engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala — One of the orphaned files carrying the most lost knowledge — ranked by size weighted by the file's role in the codebase, the same weighting behind the score above, so core code outranks equally large plumbing. A reasonable place to start a read-through before the aggregate risk above bites.
Most significant orphaned file filesystems/s3/src/main/java/org/lerch/s3fs/S3FileSystemProvider.java — One of the orphaned files carrying the most lost knowledge — ranked by size weighted by the file's role in the codebase, the same weighting behind the score above, so core code outranks equally large plumbing. A reasonable place to start a read-through before the aggregate risk above bites.

D31 · IaC & Container Security · Low IaC · ×2

REDACTED
REDACTED

D16 · Bus Factor · Off-boarding risk · ×1

Off-boarding risk: anonymized user #1 — If anonymized user #1 becomes unavailable, 7 significant file(s) lose their only recent owner: engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ExecutionStore.scala, services/src/main/scala/cromwell/services/metadata/MetadataService.scala, services/src/main/scala/cromwell/services/metadata/impl/MetadataStatisticsRecorder.scala, supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/Delocalization.scala, engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/CopyWorkflowOutputsActor.scala, engine/src/main/scala/cromwell/engine/workflow/lifecycle/OutputsLocationHelper.scala, supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/CheckpointingRunnable.scala. Pair on, review, or document these before any departure.

D16 · Bus Factor · Further sole-owners (lower concentration) · ×1

Further sole-owners (lower concentration) — 2 other contributor(s) are each the sole owner of a small amount of code below the off-boarding threshold — folded into the bus-factor score and metrics (10 single-owned of 489 analysed files in total, counted over production source files of roughly 2,400 bytes or more, excluding vendored, generated and example/demo trees and test files identified by path convention, largest first; 489 of the 1152 production source files in this repository met that bar). They are anonymized user #2 (2 file(s)), anonymized user #3 (1 file(s)) — spread or document their files in the same way, at lower priority than the named off-boarding risks above.

D19 · Documentation Quality · Documentation · ×1

Documentation: no licence statement docs/index.md — The BSD 3-Clause license is cited in the README but not shown anywhere else in the documentation. Add a LICENSE file or a link to the LICENSE.txt document so readers can confirm it applies.

D20 · ADR Quality · No ADRs found · ×1

No ADRs found — No ADRs found. No recognised ADR directory (`docs/adr/`, `docs/decisions/`, `adr/`, `docs/rfcs/`, an `ADR0001/` folder, or their siblings) exists anywhere in this tree. What was searched, so you can tell an empty log from a search that missed one: every directory under the tree (build output, dependencies and VCS metadata excepted), for a document that is either any non-index page inside a recognised ADR directory, whatever its name and however deeply nested (`docs/adr/use-postgres.md`, `docs/adr/2024/0001-x.md`); or a file anywhere whose name is ADR-shaped (`0001-use-postgres.md`, `adr-012-caching.md`); or, when neither turned anything up, a document carrying the decision-record signature (an "Architecture Decision Record" heading, or Status / Context / Decision / Consequences as section headings). A decision log that clears none of these — unnumbered files outside any recognised directory, without those headings — is not seen by this check and this row is then wrong. If that is your case, say so rather than renaming anything; otherwise, consider recording architectural decisions in `docs/adr/`.

D26 · Project Cohesion · Projects may be oversized for their cohesion · ×1

Projects may be oversized for their cohesion — 1 of 2 project(s) overshoot their size bounds, lowering Project Cohesion to 0.0/10. The most over is `(repository root)` (84917 LoC, 3586 public types across 248 directories). Review these for cohesion — draw the boundary inside the module first (group each responsibility into its own package or directory and keep the cross-boundary members non-public), since splitting a published package moves types between packages and breaks consumers.

D28 · Secrets (history) · Rotate the exposed credentials · ×1

REDACTED

D29 · Static Analysis (SAST) · REDACTED · ×1

REDACTED

D34 · Knowledge Freshness · Concentrated knowledge decay · ×1

Concentrated knowledge decay — 409 of 500 significant files have no living knowledge, while the repository is still being changed at a low rate (10 commit(s) in the last 90 days) — so this is one repo-wide knowledge-decay state, not 409 separate risks. Counted over 500 of the 1152 production source files in this repository: the rest are under the ~2,400-byte size floor this dimension measures over. The code moved on without the people who understood these files: document them or schedule a read-through before the next change lands in them.

D36 · Supply-chain Provenance & Signing · REDACTED · ×1

REDACTED

D36 · Supply-chain Provenance & Signing · REDACTED · ×1

REDACTED

D36 · Supply-chain Provenance & Signing · REDACTED · ×1

REDACTED

D36 · Supply-chain Provenance & Signing · REDACTED · ×1

REDACTED

M2 · Architecture documentation · No ADRs · ×1

No ADRs — No Architecture Decision Records found — no conventional ADR directory, no numbered `NNNN-title` documents in any markup this check reads, and nothing ADR-shaped by content. Design rationale recorded elsewhere (a design-notes tree, a mailing list, pull-request discussion) is not visible to this check and is not re-findable per decision, so a future maintainer cannot ask why one choice was made and get an answer.

P3 · Security & performance tooling · No SAST · ×1

No SAST — No static application security testing detected. For this repository's stack, add scalafix or scapegoat (or `semgrep --config=auto`, which runs on any language) as a CI step. What was searched, so you can tell an absence from a miss: the 20131 CI workflow file(s) in this repository, and the scanner and linter configuration checked in beside them. A scan that runs outside CI, one configured in your forge's web UI rather than in a committed file, or a tool whose name is none of those this check carries, is not seen — if that is your case the row is wrong, and saying so is more useful than adding a second scanner.

S1 · Web-Security Posture · No security response headers detected · ×1

No security response headers detected CromIAM/src/main/resources/application.conf:30 — No Content-Security-Policy / X-Frame-Options / X-Content-Type-Options configuration found — defense in depth, even when a reverse proxy could set them. This is reported because `application.conf` is committed to this repository and declares the server that serves it, so the configuration that would carry these headers is in this repository and was read in full. (−2.0 on this card.)

Appendix B — Reproduction & audit trail

Every external tool invocation behind a deep-scan dimension — the tool, its captured version, the exact command, how many findings it yielded, and a link to the retained raw output. To reproduce any finding: check out the same commit and run the command shown (repo-relative — never an absolute scratch path). The complete raw scanner output is retained verbatim under artifacts/raw/ (indexed in artifacts/raw/index.json); per-invocation exit codes and wall-clock durations are in sidecar.json — kept out of this table so the rendered report stays byte-identical across runs of the same commit.

Dimension	Tool	Version	Command	Findings	Raw output
D28 · Secrets (history)	gitleaks	—	gitleaks detect --no-banner --config /opt/gitleaks-rules/watchdog-gitleaks.toml --report-format json --report-path /tmp/watchdog-gitleaks-51a305a46af14f01a897870d2bc7ec41/history.json --exit-code 0 --source .	6	artifacts/raw/gitleaks-history.json
D28 · Secrets (history)	gitleaks	—	gitleaks detect --no-git --no-banner --config /opt/gitleaks-rules/watchdog-gitleaks.toml --report-format json --report-path /tmp/watchdog-gitleaks-51a305a46af14f01a897870d2bc7ec41/tree.json --exit-code 0 --source .	0	artifacts/raw/gitleaks-tree.json
D29 · Static Analysis (SAST)	semgrep	—	semgrep --config /opt/semgrep-rules/security-audit.yml --config /opt/semgrep-rules/owasp-top-ten.yml --config /opt/semgrep-rules/watchdog-sast.yml --json --quiet --timeout 10 --timeout-threshold 3 --metrics off .	44	artifacts/raw/semgrep.json
D30 · Dependency Vulnerabilities	osv-scanner	—	osv-scanner --format json --recursive .	0	artifacts/raw/osv-scanner.json
D31 · IaC & Container Security	trivy	—	trivy config --format json --quiet .	15	artifacts/raw/trivy-config.json
D32 · Data Compliance (PII/GDPR)	semgrep	—	semgrep: not applicable — No personal data was found crossing a boundary the PII/GDPR ruleset checks — nothing written to a log or console sink, placed in a URL or query string, or persisted to browser storage. That is a clean result for the LEAK surface only: this ruleset detects personal data escaping, it does not inventory the personal data a repository holds, so it is not evidence that this repository has no personal-data surface. The personal-data map (Appendix C) and the C1-C5 compliance cards are what speak to that.	0	—
D37 · Vulnerability-disclosure Policy	disclosure	—	disclosure: not applicable — No vulnerability-disclosure policy file found (SECURITY.md/.markdown/.rst/.txt at root or under .github/.forgejo/.gitea/docs, .well-known/security.txt). A coordinated-disclosure policy may live off-repo, so this is not evidenced rather than failed.	0	—
D40 · Network Egress Confinement	runtime-hardening	—	runtime-hardening: not applicable — No Kubernetes/orchestration workloads found in the repository manifests; network egress policy is a cluster-native control that may live at the platform/firewall layer, so there is nothing to assess here.	0	—
D41 · Kernel & Syscall Confinement	runtime-hardening	—	runtime-hardening: not applicable — No Kubernetes/orchestration workloads found in the repository manifests; seccomp/AppArmor/SELinux confinement is a workload-level control, so there is nothing to assess here.	0	—
D42 · Runtime Threat Enforcement	runtime-hardening	—	runtime-hardening: not applicable — No Kubernetes/orchestration workloads found in the repository manifests; runtime threat-detection and admission-control policy are cluster-level controls, so there is nothing to assess here.	0	—
D43 · Malicious Dependencies	osv-scanner	—	osv-scanner --format json --recursive .	0	artifacts/raw/osv-scanner.json

Run 01a0e92f-036f-7d20-b284-eb7320c70831 · every finding is also locatable in findings.md, and the complete scoring record (with exit codes + durations) in sidecar.json.

Broadinstitute/cromwell

Findings by grade

This survey was produced by

Executive summary

Top priorities

Diagnosis — what's actually going on

Architecture — module dependency matrix

At a glance — Code Health · 87% · Strong ·

At a glance — Architecture · 85% · Adequate · gated by D26 ·

At a glance — Maturity · 65% · Adequate · gated by D34 ·

At a glance — Readiness · 65% · Adequate · gated by P3 ·

At a glance — Security · 51% · Adequate · gated by D29, D36 ·

Security & Compliance — OWASP Top-10 mapping

Roadmap

File quality

How the grades work

Methodology & how to trust this report

Tools & methods

Run transparency — what happened this run

Limitations & what we did not check

Per-dimension blind spots

The LLM boundary

Dimensions

Frontend & cross-cutting dimensions

Reference — by lens

Appendix A — Findings (grouped)

Appendix B — Reproduction & audit trail

Downloadable artifacts