fix(sonar): remediate SonarCloud security and code-quality findings

[cryptoxdog]

Summary

Evidence-driven remediation of the SonarCloud backlog for Quantum-L9_Cognitive.Engine.Graphs (488 issues; 433 open at analyzed revision 7827d98, which matches this branch's base). Fixes target root causes with the smallest safe change, preserve behavior, and add no suppressions and no rule/quality-gate weakening. ~145 findings fixed across 78 files; the remainder are deferred with explicit rationale below (behavior/CI risk or rule-vs-architecture mismatch), per the remediation contract.

Local validation (all green, CI-pinned toolchain)

Gate	Result
ruff check . (0.15.12)	✅ All checks passed
ruff format --check .	✅ 361 files formatted
mypy engine/ (1.14.0)	✅ no issues, 139 files
tools/contract_scanner.py	✅ no violations
unit suite (-m unit)	✅ 721 passed, 4 skipped
refactored non-unit + integration tests	✅ 86 + 9 passed
verify_contracts / packet_envelope_gate / check_deprecated_imports / audit_harness	✅ pass

The 2 files requiring the py3.12-only constellation-node-sdk (tests/contracts/test_chassis_parity.py, tests/unit/test_node_app.py) run in CI on 3.12; the local env is 3.11.

Fixed

Security — workflows / Docker

• Pin GitHub Actions to immutable commit SHAs — codecov, pre-commit, trivy, create-pull-request, release-drafter, semgrep (S7637)
• supply-chain.yml: drop redundant workflow-level write perms → least-privilege contents: read; every job already scopes its own (S8233)
• k8s-deploy.yml: pass SLACK_WEBHOOK_URL via env: instead of inline ${{ secrets… }} expansion (S7636)
• coderabbit-notify.yml: interpolate PR title through shell env vars, not the Actions expression, closing a script-injection vector (S7630)
• Dockerfile.prod: add non-root l9 user (parity with the other two images) (S6471); Dockerfile: merge RUN layers (S7031)

Code quality — engine / chassis / tools / agents

• logging.exception() inside except blocks + drop redundant exc_info/message object (S8572)
• concise regex classes \d/\w where exactly equivalent (S6353)
• module constants for duplicated literals (S1192)
• math.isclose(…, abs_tol=1e-9) for float equality (S1244)
• numpy.random.Generator API + seeded RNG (S6711, S6709)
• merge-if, set.update, @total_ordering, dup-branch, lambda-capture, unused locals, regex simplification, redundant-except (S1066, S8502, S8500, S1871, S1515, S1481, S8786, S5713, S8510, S5869)

Tests

• scope pytest.raises to the single throwing call (S5778 ×31)
• narrow over-broad exception assertions to the real type + match= (S5958 ×13)
• monkeypatch for global/env state; explicit skip reasons; assert-out-of-except (S8997, S1607, S5918, S5779)

Shell / SQL

• [[ ]] conditionals, stderr redirect, drop unused var (S7688 ×11, S7677, S1481)
• explicit column lists instead of SELECT * in lineage CTEs (SelectStarCheck)

Deferred (with rationale — not fixed to protect correctness / mergeability)

• pip/poetry version-lock + --only-binary (S8541/S8544, ~99 across workflows & Dockerfiles) — requirements.txt pins constellation-node-sdk as a git URL; --only-binary=:all: would break its source install, and the security rating is all-or-nothing, so a partial pass adds churn to governed CI for zero gate benefit. Versions are already centralized in requirements-ci.txt.
• python:S3776 cognitive-complexity (60) — advisory (maintainability already rated A); 60 control-flow refactors carry real regression risk. Deferred to a dedicated follow-up rather than risk this green PR.
• python:S1172 unused params (26) — mostly handler-DI (tenant, graph_driver, domain_loader), packet-builder API, and kernel signatures; removal breaks the uniform positional dispatch / callers (Contract C-2). Interface-stability retained.
• pythonsecurity:S8707 CLI path-traversal (14) — developer CLI tools that legitimately read/write operator-supplied paths; confinement would break valid cross-directory use and cannot be locally verified as cleared. Needs an explicit path-policy decision.
• shell:S5332 clear-text (20) — all ${API_URL} / container-local http://localhost health checks; HTTPS would break the smoke tests.
• cursor_memory_client.py TLS/HTTP/IP (S5527/S4830/S4423/S5332/S1313) — intentional, documented direct-IP HTTP to a self-signed internal endpoint that bypasses Cloudflare; "fixing" breaks connectivity.
• l9-analysis.yml S8233 — file is DO NOT EDIT — managed by l9-ci-core preset.
• engine/utils/security.py S6353 (in sanitize_label) — \w is Unicode-aware; substituting it would widen the Cypher-label injection guard (Contract C-9). Correctly left as the exact ASCII class.
• engine/boot.py S7497/S7504, plsql:S1192 (RLS current_setting), S6019 ×2, S1135 ×2, S7503 async (interface-required), S125 (not dead code) — each behavior-sensitive or a rule/architecture mismatch; see commit for specifics.

Two pre-existing engine bugs surfaced (not fixed here — flagging)

1. SyncGenerator.resolve_endpoint(...) referenced by tests/integration/test_sync_handler.py does not exist; the test only passed because pytest.raises(Exception) swallowed the AttributeError.
2. engine/security/P2_9_llm_schemas.py:105 constructs ValidationError(f"…") invalidly for pydantic v2 → raises TypeError on the invalid-JSON path.

Remote verification

SonarCloud re-analysis is PENDING (runs when this revision is analyzed). The baseline quality gate is ERROR solely on new_security_rating; this PR reduces the vulnerability surface but does not claim remote closure from local reasoning.

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Generated by Claude Code

[github-actions]

❌ Too Many Reviewable Files Changed
Changed: 78 files
Limit: 50 files
Action Required: Split into multiple focused PRs

⚠️ Large PR Warning
Reviewable lines changed: 701
Warning threshold: 300 lines
Consider splitting for easier review

📋 Best Practices for Large Changes

1. Refactoring + Features: Separate into 2 PRs
2. Multiple Features: One PR per feature
3. Database + Code: Separate migration from logic
4. Generated Code: Exclude it from reviewable-size accounting

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🚫 This PR is blocked until reviewable size limits are met.

[github-actions]

L9 Audit Harness Report

• Generated: 2026-08-04T21:32:12.435540+00:00
• Repo root: /home/runner/work/Cognitive.Engine.Graphs/Cognitive.Engine.Graphs
• Overall result: ✅ PASSED
• Exit code: 0

Step Results

Step	Status	Exit Code	Notes
Architecture Audit	✅ Passed	0
Spec Coverage	✅ Passed	0
Contract Wiring	✅ Passed	0

Architecture Audit Findings

Severity	Count
🔴 CRITICAL	0
🟠 HIGH	0
🟡 MEDIUM	25
🔵 LOW	0

See artifacts/audit_report.md for full details.

Spec Coverage

• ✅ Implemented: 37
• ⚠️ Partial: 9
• ❌ Missing: 0
• Total features: 46

Category	Implemented	Partial	Missing	Total
gates	10	0	0	10
scoring	7	0	0	7
v1.1_node	2	0	0	2
v1.1_edge	2	0	0	2
v1.1_action	0	2	0	2
v1.1_scoring	1	1	0	2
action_handler	0	6	0	6
gds_algorithm	5	0	0	5
research_pattern	10	0	0	10

See artifacts/coverage_report.md for full details.

Next Steps

All checks passed. Safe to merge.

[Copilot]

Pull request overview

This PR performs broad, evidence-driven remediation of SonarCloud security and code-quality findings across the CEG repository, spanning engine runtime code, tooling, tests, scripts, containers, and GitHub Actions workflows.

Changes:

• Hardens CI/CD supply chain by pinning GitHub Actions to immutable SHAs and tightening workflow-level permissions.
• Refactors multiple code paths for improved robustness/clarity (e.g., exception logging via logger.exception, reduced duplicated literals, safer float comparisons, small control-flow simplifications).
• Updates tests to narrow exception assertions and reduce over-broad pytest.raises(...) scopes.

Reviewed changes

Copilot reviewed 78 out of 78 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
tools/validate_domain.py	Simplifies exception handling in compliance checks.
tools/spec_extract.py	Centralizes glob/filename constants for spec feature extraction outputs.
tools/packet_envelope_gate.py	Simplifies exception tuple in contract-gate parsing.
tools/infra/precommit_smoke.sh	Removes unused variable in container health check helper.
tools/infra/docker_validate.sh	Sends failure summary to stderr.
tools/contract_scanner.py	Extracts repeated literals into module constants for contract rules.
tools/check_deprecated_imports.py	Tightens regex for deprecated import detection.
tools/audit_harness.py	Extracts step-name constant; simplifies severity icon selection.
tools/audit_engine.py	Collapses nested conditionals for required-any token enforcement.
tests/unit/test_sync_projection.py	Narrows pytest.raises scope by isolating the throwing call.
tests/unit/test_projection_outcome_schemas.py	Narrows pytest.raises scope by isolating the throwing call.
tests/unit/test_plasticos_spec_authority.py	Uses explicit pytest.skip(...) for non-authoritative entries.
tests/unit/test_packet_envelope.py	Narrows exception assertions to ValidationError with match=.
tests/unit/test_hgkr_schema.py	Narrows pytest.raises scope by isolating the throwing call.
tests/unit/test_gates_all_types.py	Avoids inlined mocks; clarifies instantiation failure case.
tests/unit/test_domain_loader.py	Asserts specific domain-spec exception type + message.
tests/unit/test_config_schema.py	Reduces duplicated literals by pre-building shared node lists.
tests/test_scoring_extended.py	Narrows pytest.raises scope; avoids repeated factory calls.
tests/test_config_loader.py	Avoids repeated loader construction to narrow exception scope.
tests/test_compliance_engine.py	Avoids repeated engine construction to narrow exception scope.
tests/test_algorithmic_upgrades.py	Narrows exception types; uses monkeypatch for env state.
tests/invariants/test_configuration.py	Narrows to ValidationError with message match.
tests/integration/test_sync_handler.py	Narrows assertion to the actual raised exception type.
tests/integration/test_handlers.py	Narrows pytest.raises scope around asyncio.run(...).
tests/integration/test_admin_handler.py	Allows either raising or error-dict return shape (explicit branching).
tests/gap_fixes/test_gap5_audit.py	Uses monkeypatch instead of mutating module globals.
tests/contracts/test_templates.py	Adds explicit reasons to pytest.skip(...).
scripts/scripts-setup.sh	Uses [[ ... ]] tests for safer shell conditionals.
scripts/scripts-seed.sh	Uses [[ ... ]] tests; minor conditional cleanup.
scripts/scripts-migrate.sh	Uses [[ ... ]] tests; minor conditional cleanup.
scripts/scripts-health.sh	Uses [[ ... ]] tests for status-code check.
scripts/scripts-gds-trigger.sh	Uses [[ ... ]] tests for JOB dispatch.
scripts/scripts-build.sh	Uses [[ ... ]] tests for account-id guard.
engine/traversal/resolver.py	Uses logger.exception to preserve traceback on resolution failures.
engine/traversal/assembler.py	Regex simplification for label reference extraction.
engine/security/P2_9_llm_schemas.py	Tightens schema-hint sanitization regex (removes redundancy).
engine/security/_5_llm_security.py	Uses logger.exception when JSON/schema validation fails.
engine/resolution/resolver.py	Uses set.update(...) instead of a loop.
engine/personas/synthesis.py	Uses math.isclose for float-zero comparison.
engine/personas/composer.py	Uses math.isclose for float-zero comparison.
engine/packet/packet_store.sql	Replaces SELECT * with explicit column lists in lineage functions.
engine/kge/ensemble.py	Extracts repeated “no scores” error string to a constant.
engine/kge/compound_e3d.py	Switches to numpy.random.Generator; minor loop simplification.
engine/kge/beam_search.py	Adds ordering support via @total_ordering; seeds RNG in scoring helper.
engine/intake/intake_compiler.py	Uses math.isclose for float-zero comparison.
engine/intake/impact_reporter.py	Simplifies gate passability conditional.
engine/intake/crm_field_scanner.py	Extracts repeated separator regex into a constant.
engine/health/health_report.py	Collapses nested tier conditional.
engine/handlers.py	Regex simplification for property validation; uses logger.exception on match failures.
engine/gds/scheduler.py	Uses logger.exception for job failures and drop/pre-drop errors.
engine/gates/compiler.py	Extracts AND joiner constant; uses math.isclose for relaxed-penalty checks.
engine/feedback/signal_weights.py	Uses math.isclose for float-zero comparison.
engine/diagnostics/fingerprint.py	Avoids repeated dict lookup in max(...) key function.
engine/contract_enforcement.py	Collapses nested conditionals for envelope_hash requirement.
engine/config/units.py	Uses logger.exception to preserve traceback on formula evaluation failure.
engine/config/loader.py	Extracts spec.yaml constant used for domain discovery/loading.
engine/compliance/pii.py	Simplifies numeric regex classes; avoids variable shadowing; uses logger.exception.
engine/compliance/audit.py	Uses logger.exception for persistence failures.
engine/auth/capabilities.py	Extracts repeated permission strings to constants; uses math.isclose for expiry.
Dockerfile.prod	Adds non-root runtime user for prod image.
Dockerfile	Merges RUN layers for entrypoint chmod + user creation/chown.
chassis/pii.py	Simplifies numeric regex classes in PII patterns.
chassis/chassis_app.py	Uses logger.exception on health route failure.
chassis/auth/auth.py	Collapses nested bypass-key checks into a single condition.
chassis/actions.py	Uses logger.exception on engine handler import failure.
agents/cursor/ingest_lessons.py	Extracts duplicated timestamp literal into a constant; removes unused capture.
agents/cursor/gmp_meta_learning.py	Avoids unused locals; adjusts lambda capture; awaits calls directly.
agents/cursor/cursor_session_hooks.py	Simplifies tool-id checks for file-touching actions.
agents/cursor/cursor_memory_client.py	Extracts JSON content-type literal into a constant.
.github/workflows/supply-chain.yml	Least-privilege workflow-level permissions; job-level scopes expected.
.github/workflows/release-drafter.yml	Pins action to immutable commit SHA.
.github/workflows/lint-autofix.yml	Pins action to immutable commit SHA.
.github/workflows/k8s-deploy.yml	Moves Slack webhook secret into env var usage to reduce injection risk.
.github/workflows/docker-build.yml	Pins Trivy action to immutable commit SHA.
.github/workflows/dev-layer-gmp.yml	Pins Codecov action to immutable commit SHA.
.github/workflows/coderabbit-notify.yml	Avoids direct expression interpolation in shell heredoc content.
.github/workflows/ci.yml	Pins pre-commit and Codecov actions to immutable commit SHAs.
.github/workflows/ci-quality.yml	Pins Semgrep and Codecov actions to immutable commit SHAs.

Suppressed comments (1)

agents/cursor/gmp_meta_learning.py:791

• Same issue as above: this log line is not formatted and active is no longer assigned. Assign the awaited result and log the actual count (or remove the count wording).

    # Get active heuristics for next GMP
    await engine.get_active_heuristics()
    logger.info("active heuristics: {len(active)}")

[sonarqubecloud]

Quality Gate passed

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[Copilot]

Pull request overview

Copilot reviewed 78 out of 78 changed files in this pull request and generated no new comments.

Suppressed comments (1)

engine/security/_5_llm_security.py:157

• pydantic.ValidationError can’t be instantiated with a plain string in Pydantic v2, so raise ValidationError(f"...") will itself raise a TypeError, masking the real JSON parse failure. Raise a standard exception (e.g., ValueError) or construct a proper Pydantic ValidationError via ValidationError.from_exception_data(...).