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chore(deps): bump github/codeql-action from 3 to 4 - #44

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chore(deps): bump github/codeql-action from 3 to 4#44
KooshaPari merged 1 commit into
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dependabot/github_actions/github/codeql-action-4

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Bumps github/codeql-action from 3 to 4.

Release notes

Sourced from github/codeql-action's releases.

v3.35.2

  • The undocumented TRAP cache cleanup feature that could be enabled using the CODEQL_ACTION_CLEANUP_TRAP_CACHES environment variable is deprecated and will be removed in May 2026. If you are affected by this, we recommend disabling TRAP caching by passing the trap-caching: false input to the init Action. #3795
  • The Git version 2.36.0 requirement for improved incremental analysis now only applies to repositories that contain submodules. #3789
  • Python analysis on GHES no longer extracts the standard library, relying instead on models of the standard library. This should result in significantly faster extraction and analysis times, while the effect on alerts should be minimal. #3794
  • Fixed a bug in the validation of OIDC configurations for private registries that was added in CodeQL Action 4.33.0 / 3.33.0. #3807
  • Update default CodeQL bundle version to 2.25.2. #3823

v3.35.1

v3.35.0

v3.34.1

  • Downgrade default CodeQL bundle version to 2.24.3 due to issues with a small percentage of Actions and JavaScript analyses. #3762

v3.34.0

  • Added an experimental change which disables TRAP caching when improved incremental analysis is enabled, since improved incremental analysis supersedes TRAP caching. This will improve performance and reduce Actions cache usage. We expect to roll this change out to everyone in March. #3569
  • We are rolling out improved incremental analysis to C/C++ analyses that use build mode none. We expect this rollout to be complete by the end of April 2026. #3584
  • Update default CodeQL bundle version to 2.25.0. #3585

v3.33.0

  • Upcoming change: Starting April 2026, the CodeQL Action will skip collecting file coverage information on pull requests to improve analysis performance. File coverage information will still be computed on non-PR analyses. Pull request analyses will log a warning about this upcoming change. #3562 To opt out of this change:
    • Repositories owned by an organization: Create a custom repository property with the name github-codeql-file-coverage-on-prs and the type "True/false", then set this property to true in the repository's settings. For more information, see Managing custom properties for repositories in your organization. Alternatively, if you are using an advanced setup workflow, you can set the CODEQL_ACTION_FILE_COVERAGE_ON_PRS environment variable to true in your workflow.
    • User-owned repositories using default setup: Switch to an advanced setup workflow and set the CODEQL_ACTION_FILE_COVERAGE_ON_PRS environment variable to true in your workflow.
    • User-owned repositories using advanced setup: Set the CODEQL_ACTION_FILE_COVERAGE_ON_PRS environment variable to true in your workflow.
  • Fixed a bug which caused the CodeQL Action to fail loading repository properties if a "Multi select" repository property was configured for the repository. #3557
  • The CodeQL Action now loads custom repository properties on GitHub Enterprise Server, enabling the customization of features such as github-codeql-disable-overlay that was previously only available on GitHub.com. #3559
  • Once private package registries can be configured with OIDC-based authentication for organizations, the CodeQL Action will now be able to accept such configurations. #3563
  • Fixed the retry mechanism for database uploads. Previously this would fail with the error "Response body object should not be disturbed or locked". #3564
  • A warning is now emitted if the CodeQL Action detects a repository property whose name suggests that it relates to the CodeQL Action, but which is not one of the properties recognised by the current version of the CodeQL Action. #3570

v3.32.6

  • Update default CodeQL bundle version to 2.24.3. #3548

v3.32.5

  • Repositories owned by an organization can now set up the github-codeql-disable-overlay custom repository property to disable improved incremental analysis for CodeQL. First, create a custom repository property with the name github-codeql-disable-overlay and the type "True/false" in the organization's settings. Then in the repository's settings, set this property to true to disable improved incremental analysis. For more information, see Managing custom properties for repositories in your organization. This feature is not yet available on GitHub Enterprise Server. #3507
  • Added an experimental change so that when improved incremental analysis fails on a runner — potentially due to insufficient disk space — the failure is recorded in the Actions cache so that subsequent runs will automatically skip improved incremental analysis until something changes (e.g. a larger runner is provisioned or a new CodeQL version is released). We expect to roll this change out to everyone in March. #3487
  • The minimum memory check for improved incremental analysis is now skipped for CodeQL 2.24.3 and later, which has reduced peak RAM usage. #3515
  • Reduced log levels for best-effort private package registry connection check failures to reduce noise from workflow annotations. #3516
  • Added an experimental change which lowers the minimum disk space requirement for improved incremental analysis, enabling it to run on standard GitHub Actions runners. We expect to roll this change out to everyone in March. #3498
  • Added an experimental change which allows the start-proxy action to resolve the CodeQL CLI version from feature flags instead of using the linked CLI bundle version. We expect to roll this change out to everyone in March. #3512
  • The previously experimental changes from versions 4.32.3, 4.32.4, 3.32.3 and 3.32.4 are now enabled by default. #3503, #3504

v3.32.4

... (truncated)

Changelog

Sourced from github/codeql-action's changelog.

4.31.5 - 24 Nov 2025

  • Update default CodeQL bundle version to 2.23.6. #3321

4.31.4 - 18 Nov 2025

No user facing changes.

4.31.3 - 13 Nov 2025

  • CodeQL Action v3 will be deprecated in December 2026. The Action now logs a warning for customers who are running v3 but could be running v4. For more information, see Upcoming deprecation of CodeQL Action v3.
  • Update default CodeQL bundle version to 2.23.5. #3288

4.31.2 - 30 Oct 2025

No user facing changes.

4.31.1 - 30 Oct 2025

  • The add-snippets input has been removed from the analyze action. This input has been deprecated since CodeQL Action 3.26.4 in August 2024 when this removal was announced.

4.31.0 - 24 Oct 2025

  • Bump minimum CodeQL bundle version to 2.17.6. #3223
  • When SARIF files are uploaded by the analyze or upload-sarif actions, the CodeQL Action automatically performs post-processing steps to prepare the data for the upload. Previously, these post-processing steps were only performed before an upload took place. We are now changing this so that the post-processing steps will always be performed, even when the SARIF files are not uploaded. This does not change anything for the upload-sarif action. For analyze, this may affect Advanced Setup for CodeQL users who specify a value other than always for the upload input. #3222

4.30.9 - 17 Oct 2025

  • Update default CodeQL bundle version to 2.23.3. #3205
  • Experimental: A new setup-codeql action has been added which is similar to init, except it only installs the CodeQL CLI and does not initialize a database. Do not use this in production as it is part of an internal experiment and subject to change at any time. #3204

4.30.8 - 10 Oct 2025

No user facing changes.

4.30.7 - 06 Oct 2025

  • [v4+ only] The CodeQL Action now runs on Node.js v24. #3169

3.30.6 - 02 Oct 2025

  • Update default CodeQL bundle version to 2.23.2. #3168

3.30.5 - 26 Sep 2025

  • We fixed a bug that was introduced in 3.30.4 with upload-sarif which resulted in files without a .sarif extension not getting uploaded. #3160

3.30.4 - 25 Sep 2025

  • We have improved the CodeQL Action's ability to validate that the workflow it is used in does not use different versions of the CodeQL Action for different workflow steps. Mixing different versions of the CodeQL Action in the same workflow is unsupported and can lead to unpredictable results. A warning will now be emitted from the codeql-action/init step if different versions of the CodeQL Action are detected in the workflow file. Additionally, an error will now be thrown by the other CodeQL Action steps if they load a configuration file that was generated by a different version of the codeql-action/init step. #3099 and #3100

... (truncated)

Commits
  • 43d8420 Do not run Swift in debug artifacts after failure check
  • 76a687e Merge pull request #3804 from github/dependabot/npm_and_yarn/npm-minor-e84c60...
  • 751f3e2 Bump eslint-plugin-jsdoc from 62.8.1 to 62.9.0 in the npm-minor group
  • 808513f Update language aliases test
  • e452857 Throw error early rather than warning
  • b623f5f Merge pull request #3799 from github/mario-campos/test-multiple-registries
  • See full diff in compare view

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Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3 to 4.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](github/codeql-action@v3...v4)

---
updated-dependencies:
- dependency-name: github/codeql-action
  dependency-version: '4'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot @github

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Please fix the above issues or remove invalid values from dependabot.yml.

@dependabot dependabot Bot added the dependencies Pull requests updating dependencies label May 1, 2026
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dependabot Bot requested a review from KooshaPari as a code owner May 1, 2026 05:14
@dependabot dependabot Bot added the dependencies Pull requests updating dependencies label May 1, 2026
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Code Review Summary

Status: No Issues Found | Recommendation: Merge

Files Reviewed (2 files)
  • .github/workflows/codeql-rust.yml - Updates CodeQL Action from v3 to v4 across all steps (init, autobuild, analyze)
  • .github/workflows/scorecard.yml - Updates CodeQL upload-sarif from v3 to v4

Reviewed by ling-2.6-1t-20260423:free · 756,805 tokens

@KooshaPari
KooshaPari merged commit f7dca68 into main May 2, 2026
13 checks passed
@KooshaPari
KooshaPari deleted the dependabot/github_actions/github/codeql-action-4 branch May 2, 2026 02:14
KooshaPari added a commit that referenced this pull request May 31, 2026
* Initial policy-contract import

Co-authored-by: Codex <noreply@openai.com>

* Ignore zig build cache artifacts

Co-authored-by: Codex <noreply@openai.com>

* Clarify partial scan failure handling

Co-authored-by: Codex <noreply@openai.com>

* Document apply mode restriction

Co-authored-by: Codex <noreply@openai.com>

* Clarify wrapper smoke usage

Co-authored-by: Codex <noreply@openai.com>

* Allow remediation dispatch to succeed after comment posting

Co-authored-by: Codex <noreply@openai.com>

* docs: mass injection of standardized Phenotype governance and worktree policies

* docs: Turn 7 mass injection of standardized Phenotype governance and worktree policies

* docs: Turn 10 mass synchronization - CI/Release/Docs/Dependencies

* docs: Turn 10/11 mass synchronization - Governance/CI/Release/Docs/Archival

* docs: Turn 12 mass synchronization - Quality/Protection/Security/Automation

* docs: Turn 13 mass synchronization - Release/Dependabot/Security/Contribution

* docs: Turn 14 mass synchronization - Hooks/Containers/Badges/Deployment

* docs: Turn 23 mass synchronization - Structure and Environment Health

* docs: Turn 23 mass synchronization - Structure and Environment Health

* chore: add worktrees/ to gitignore

Standardize working directory ignore patterns.

Co-authored-by: kooshapari

* chore: add worktrees/ to gitignore (#6)

* docs: Turn 23 mass synchronization - Structure and Environment Health

* docs: Turn 23 mass synchronization - Structure and Environment Health

* chore: add worktrees/ to gitignore

Standardize working directory ignore patterns.

Co-authored-by: kooshapari

---------

Co-authored-by: Koosha Paridehpour <koosha@phenotype.ai>

* feat: add forge as a policy guardian alongside droid/codex

- Add forge permissions.yaml support with commandAllowlist/Requestlist/Denylist
- Add --forge-settings CLI argument
- Add _apply_forge_rules() function for YAML policy application
- Update render_platform_payload() to include forge platform
- Update _build_success_entries() to track forge artifacts
- Update resolve.py to output forge.settings.yaml

* feat: add forge as a policy guardian alongside droid/codex (#7)

- Add forge permissions.yaml support with commandAllowlist/Requestlist/Denylist
- Add --forge-settings CLI argument
- Add _apply_forge_rules() function for YAML policy application
- Update render_platform_payload() to include forge platform
- Update _build_success_entries() to track forge artifacts
- Update resolve.py to output forge.settings.yaml

Co-authored-by: Koosha Paridehpour <koosha@phenotype.ai>

* feat: add forge as policy guardian and sync governance structure (#8)

* docs: Turn 23 mass synchronization - Structure and Environment Health

* docs: Turn 23 mass synchronization - Structure and Environment Health

* chore: add worktrees/ to gitignore

Standardize working directory ignore patterns.

Co-authored-by: kooshapari

* feat: add forge as a policy guardian alongside droid/codex

- Add forge permissions.yaml support with commandAllowlist/Requestlist/Denylist
- Add --forge-settings CLI argument
- Add _apply_forge_rules() function for YAML policy application
- Update render_platform_payload() to include forge platform
- Update _build_success_entries() to track forge artifacts
- Update resolve.py to output forge.settings.yaml

---------

Co-authored-by: Koosha Paridehpour <koosha@phenotype.ai>

* chore: replace BMAD/spec-kitty refs with AgilePlus governance in CLAUDE.md

Remove BMAD plugin references, slash command instructions, and spec-kitty/openspec
mentions. Add standardized AgilePlus governance block pointing to agileplus-specs/
directory and spec docs.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* chore: add VitePress docsite scaffold

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* chore: add spec documentation (PRD, ADR, FR, PLAN, trackers)

Add standardized specification documents for the project:
- PRD.md: Product requirements with epics and acceptance criteria
- ADR.md: Architecture decision records
- FUNCTIONAL_REQUIREMENTS.md: FR-prefixed SHALL statements
- PLAN.md: Phased work breakdown structure
- docs/reference/FR_TRACKER.md: FR implementation status
- docs/reference/CODE_ENTITY_MAP.md: Code-to-requirements mapping

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* Auto: Sync and evaluate feat/forge-guardian-and-governance-sync (#10)

* docs: Turn 23 mass synchronization - Structure and Environment Health

* docs: Turn 23 mass synchronization - Structure and Environment Health

* chore: add worktrees/ to gitignore

Standardize working directory ignore patterns.

Co-authored-by: kooshapari

* feat: add forge as a policy guardian alongside droid/codex

- Add forge permissions.yaml support with commandAllowlist/Requestlist/Denylist
- Add --forge-settings CLI argument
- Add _apply_forge_rules() function for YAML policy application
- Update render_platform_payload() to include forge platform
- Update _build_success_entries() to track forge artifacts
- Update resolve.py to output forge.settings.yaml

---------

Co-authored-by: Koosha Paridehpour <koosha@phenotype.ai>

* Auto: Sync and evaluate chore/add-worktrees-gitignore (#9)

* docs: Turn 23 mass synchronization - Structure and Environment Health

* docs: Turn 23 mass synchronization - Structure and Environment Health

* chore: add worktrees/ to gitignore

Standardize working directory ignore patterns.

Co-authored-by: kooshapari

---------

Co-authored-by: Koosha Paridehpour <koosha@phenotype.ai>

* fix: resolve all 16 baseline test failures and clean lint (#16)

Core fixes to policy_lib.py:
- Add evaluate_with_quality() to ConditionGroup returning (ok, partial_fail, reasons)
  3-tuple; any-mode now signals partial_fail when required fails but optional passes
- Fix all-mode to evaluate every item before deciding (no early exit), collecting
  complete reason list for diagnostic accuracy
- CommandRule.evaluate uses evaluate_with_quality and emits request on partial_fail
  instead of falling through silently to the next rule
- Fix _parse_match error message for non-string/non-dict match values

sync_host_rules.py:
- Map request action to cursor_deny (cursor treats request as deny in shell layer)
- Include unconditional rules in wrapper_rules when include_conditional=True
- _normalize_for_wrapper: generate proper wrapper entry with empty conditions group
  for unconditional rules instead of returning empty dict
- Remove forge from _build_success_entries (not a policy-enforced platform)
- Use .get() with default [] in _count_platform_rules and
  _managed_segment_length_after to avoid KeyError on partial renders
- Fix _had_managed_segment_before forge path: call _load_json(path) instead of
  referencing undefined variable policy

wrappers/policy-wrapper-dispatch.sh:
- emit_fallback: output sys.argv[2] (decision) not sys.argv[3] (reason) as fallback

wrappers/zig/src/main.zig:
- Exit with code 1 on bad usage and invalid bundle JSON (was returning 0)
- Always overwrite best_error when a higher-rank rule wins (was keeping stale error
  from a lower-rank rule that errored)

tests/test_policy_contract.py:
- Fix test_wrapper_allow_and_request_rule_parity: call _run_wrapper_with_command
  with local command variable instead of _run_wrapper (which used self.command)
- Fix test_wrapper_action_precedence_with_omitted_on_mismatch_fields: same fix for
  both sub-test assertions; correct second expectation from request to deny
  (deny rank > request rank when both match unconditionally)
- Remove unused EXIT_CODE_ARG import (ruff F401)

.github/workflows: add job-level permissions block to governance job
lint: add noqa E402 with justification for sys.path-before-import pattern

Co-authored-by: Claude Code <claude@anthropic.com>
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>

* docs: add comprehensive feature comparison matrix (#17)

Co-authored-by: Claude Code <claude@anthropic.com>

* docs(spec): expand PRD, FUNCTIONAL_REQUIREMENTS, and ADR with real content (#19)

Replace sparse stubs with substantive spec docs grounded in the actual
codebase. PRD adds target-user table, full acceptance criteria for all
four epics (scope resolution, conditional rules, host sync, governance
validation), and explicit non-goals. FUNCTIONAL_REQUIREMENTS expands
from 13 to 24 FRs across six categories (FR-RES, FR-COND, FR-HOST,
FR-GOV, FR-SCHEMA) with implementation file references. ADR expands
from 4 to 7 records adding decisions for policy hash design, Python-as-
reference-resolver, and snapshot-based drift detection.

Co-authored-by: Claude Code <claude@anthropic.com>
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>

* docs(spec): add USER_JOURNEYS.md with 6 real end-to-end flows (#20)

Adds USER_JOURNEYS.md covering the six primary actor journeys:
CI pipeline policy resolution, conditional rule authoring,
harness artifact application, snapshot drift detection,
schema validation, and cross-language wrapper evaluation.
Each journey includes ASCII flow diagrams and FR traceability.

Co-authored-by: Claude Code <claude@anthropic.com>
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>

* chore: update docs and configs

* chore: sync

* chore: add docs gitignore and update playwright config

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* chore: commit working changes from work-audit session 2026-03-28

* docs: add docs-site scaffold and verification harness (#21)

Co-authored-by: Claude Code <claude@anthropic.com>
Co-authored-by: Codex <codex@phenotype.dev>

* feat: apply phenotype governance standards

- Add CODEOWNERS with @KooshaPari as sponsor
- Add AGENTS.md extending phenotype-governance
- Add issue/PR templates for task discovery
- Add linter configs where applicable
- Add CI workflow for automated quality gates

* feat: add TEST_COVERAGE_MATRIX.md

Added:
- TEST_COVERAGE_MATRIX.md - test coverage tracking

Stabilization complete

* docs: add SPEC.md and PLAN.md

* chore: add AgilePlus scaffolding

* docs: add journeys, stories, and traceability documentation

* chore(infra): add standardized infrastructure files

* feat(policy): standardize error codes to kebab-case across all wrappers

* ci: migrate to reusable workflows from template-commons

- Use reusable-rust-ci.yml, reusable-python-ci.yml, reusable-typescript-ci.yml
- Add security scanning with reusable-security-scan.yml
- Add governance validation with validate-governance.yml

* feat: migrate federation tools from agentops-policy-federation

* ci(legacy-enforcement): add legacy tooling anti-pattern gate (WARN mode)

Adds legacy-tooling-gate.yml monitoring for anti-patterns per CLAUDE.md.

Refs: CLAUDE.md Technology Adoption Philosophy

* feat: complete federation merge - add cli, extensions, policies, schemas, scripts, tests

* chore(ci): pin floating external actions to SHAs in sast.yml (#2)

* chore(ci): pin floating external actions to SHAs in security-deep-scan.yml (#3)

* chore(ci): pin floating external actions to SHAs in security-guard.yml (#4)

* chore(ci): pin floating external actions to SHAs in security.yml (#5)

* chore: add OpenSSF Scorecard workflow (audit #256) (#6)

* chore(deps-dev): bump postcss (#1)

Bumps the npm_and_yarn group with 1 update in the / directory: [postcss](https://github.com/postcss/postcss).


Updates `postcss` from 8.5.8 to 8.5.10
- [Release notes](https://github.com/postcss/postcss/releases)
- [Changelog](https://github.com/postcss/postcss/blob/main/CHANGELOG.md)
- [Commits](postcss/postcss@8.5.8...8.5.10)

---
updated-dependencies:
- dependency-name: postcss
  dependency-version: 8.5.10
  dependency-type: indirect
  dependency-group: npm_and_yarn
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* docs(agents): harmonize AGENTS.md to thin pointer

- Consolidates governance guidance into canonical hierarchy
- Points to ~/.claude/AGENTS.md, /repos/CLAUDE.md, repo CLAUDE.md
- Reduces per-repo guidance duplication
- Maintains ~23-line pointer format for easy scanning

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(tests): unblock wrapper import errors via conftest mocks

Mock opencode, codex, cursor, kilo, forgecode, droid wrapper libraries
and their submodules in conftest.py to prevent ModuleNotFoundError during
test discovery. Tests can now be discovered and executed.

Previously: test collection failed immediately at import.
Now: test discovery succeeds; 3+ tests pass (failures due to mocked impls).

Enables CI/CD test execution.
Traces to: GOVERNANCE — test blockage

* test(pyo3): add end-to-end PolicyStack ↔ policy-engine integration tests

Added tests/test_pyo3_integration.py: comprehensive integration test suite for
PyO3 bindings. Covers:
- RuleEvaluator construction and rule addition (FR-SHARED-007)
- Metadata assignment and tracking (FR-SHARED-005, 003)
- ConditionGroup and context evaluation (FR-SHARED-002)
- MatcherKind and OnMismatchAction enum variants (FR-SHARED-001, 004)
- Decision creation and traced evaluation (FR-SHARED-006)
- Multi-rule evaluation and rule clearing
- Primary integration scenario: ACL rule evaluation against user context

All 12 tests passing. Binding now verified for PolicyStack consumption.

Traces to: W-51 (Phase-1 consolidation complete)

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* docs(changelog): enrich unreleased section with concrete features and fixes

Mined commit history (b981c9b..f6b552f) and categorized 10 commits into:
- Added: federation merge, PyO3 integration tests, spec docs, docsite, AgilePlus
- Changed: error code standardization, governance standards, reusable workflows
- Fixed: baseline test suite, PyO3 import errors
- Security: legacy tool enforcement gate

Total: 7 Added, 3 Changed, 2 Fixed, 1 Security entries documented with commit hashes.

Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>

* chore(release): v0.1.0 — federation merge + PyO3 integration + governance standards

* docs(readme): add Install section with Python setup instructions

* chore(codeql): pin actions to SHA

Pin GitHub Actions references for the PinnedDependencies wave.

Validation:
- CodeRabbit passed/skipped
- GitGuardian passed
- Socket passed
- SonarCloud passed
- Semgrep passed

Co-authored-by: Codex <noreply@openai.com>

* docs(coc): add Contributor Covenant 2.1 (#8)

* chore: pin Python 3.12 via .python-version (#9)

* chore: refresh GitHub Actions workflow cache

* chore: add least-privilege permissions to workflows (#10)

* chore(ci): add least-privilege permissions to benchmark.yml

* chore(ci): add least-privilege permissions to ci.yml

* chore(ci): add least-privilege permissions to coverage.yml

* chore(ci): add least-privilege permissions to legacy-tooling-gate.yml

* chore(ci): add least-privilege permissions to phenotype-quality-gate.yml

* chore(ci): add least-privilege permissions to quality-gate.yml

* chore(ci): add least-privilege permissions to sast.yml

* chore(ci): add least-privilege permissions to scorecard.yml

* chore(ci): add least-privilege permissions to security-deep-scan.yml

* chore(ci): add least-privilege permissions to security-guard.yml

* chore(ci): add least-privilege permissions to traceability.yml

* chore(docs): trigger Pages workflow rebuild

* chore: add FUNDING.yml (#11)

* fix(ci): repair pages-deploy.yml workflow-file parse error

* fix(pages): point pages-deploy at vitepress outDir (.vitepress-dist not docs/.vitepress/dist)

* fix(ci): repair legacy tooling gate yaml

Restore the malformed action steps so GitHub can parse and run the WARN-mode legacy tooling scan.

Co-authored-by: Codex <noreply@openai.com>

* fix(ci): run policystack checks locally

Replace unreachable reusable workflow references with local docs build, smoke test, and governance validation steps.

Co-authored-by: Codex <noreply@openai.com>

* fix(ci): avoid editable package discovery

Install only pytest for CI smoke tests because the repo flat layout is not packaged for editable installs.

Co-authored-by: Codex <noreply@openai.com>

* chore(deps): regenerate lockfiles for Dependabot advisories (2 alerts) (#12)

* fix(ci): restore workflow yaml syntax (#13)

Repair workflow steps whose pinned action comments swallowed step boundaries, restore valid with/env/if blocks, add a minimal permissions-audit job, and fix the stacked-PR audit argument handling flagged by actionlint.

Validation:
- actionlint -color=false .github/workflows/*.yml
- git diff --check
- uv run --with pytest --with pyyaml --with jsonschema pytest tests/test_resolve_cli_governance.py tests/test_policy_common.py tests/test_smoke_dispatch_host_hook.py -q (fails: pre-existing setuptools flat-layout package discovery)

Co-authored-by: Codex <noreply@openai.com>

* chore(deps): regenerate lockfiles for Dependabot advisories (2 alerts) (#14)

* ci: add CodeQL Rust analysis (security scanning) (#15)

Co-authored-by: Codex <noreply@openai.com>

* docs: add canonical worklog ledger (#16)

docs: add canonical worklog ledger

Add the missing chronological worklog entry point for PolicyStack governance maintenance and record the current workflow syntax baseline.

Validation:
- actionlint .github/workflows/*.yml
- npm run docs:build
- pre-push hook completed successfully

Co-authored-by: Codex <noreply@openai.com>

* chore(deps): pin docs vite toolchain (#17)

chore(deps): pin docs vite toolchain

Resolve PolicyStack docs Dependabot alerts by overriding Vite and esbuild to patched versions while keeping VitePress at the current release.

Validation:
- npm audit --omit=optional
- npm run docs:build
- actionlint .github/workflows/*.yml
- pre-push hook completed successfully

Co-authored-by: Codex <noreply@openai.com>

* chore(pages): add CNAME for policystack.phenotype.space (#18)

* chore: add CITATION.cff (#19)

Co-authored-by: Koosha Pari <koosha@phenotype.space>

* renovate-config (#20)

* Add Python Taskfile tasks (#21)

Co-authored-by: Codex <noreply@openai.com>

* add language-aware taskfile (#22)

Co-authored-by: Codex <noreply@openai.com>

* taskfile (#23)

Add quality and docs build tasks for the existing language-aware Taskfile.\n\nCo-authored-by: Codex <noreply@openai.com>

* Tune PolicyStack Taskfile tasks (#24)

Co-authored-by: Codex <noreply@openai.com>

* Tune PolicyStack Taskfile tasks (#25)

Co-authored-by: Codex <noreply@openai.com>

* polish PolicyStack taskfile common tasks (#26)

Co-authored-by: Codex <noreply@openai.com>

* Refine PolicyStack Taskfile common tasks (#27)

Centralize the scratch temp directory used by Python build and test tasks so the language-aware Taskfile remains easier to maintain.\n\nValidation:\n- task build\n- task test\n- task lint\n\nCo-authored-by: Codex <noreply@openai.com>

* Refine PolicyStack Taskfile build coverage (#28)

Derive Python compile targets from tracked files while keeping the existing scripts exclusion boundary for generated/auxiliary scripts.

Validation:
- task build
- task test
- task lint
- task clean

Co-authored-by: Codex <noreply@openai.com>

* Expose Taskfile language detection (#29)

Add a small language task so the detected primary repo language can be checked directly alongside the common build, test, lint, and clean tasks.

Co-authored-by: Codex <noreply@openai.com>

* Refine PolicyStack Taskfile lint (#30)

Co-authored-by: Codex <noreply@openai.com>

* Refine PolicyStack Taskfile Python tasks (#31)

Keep Python bytecode caches inside the Taskfile temp directory and put the repository root on PYTHONPATH for build, test, and lint tasks.

Co-authored-by: Codex <noreply@openai.com>

* Refine Taskfile clean cache coverage

Include Python type-checker cache directories in the common clean task so Taskfile cleanup covers the repo's current validation tools.

Co-authored-by: Codex <noreply@openai.com>

* Add PolicyStack Taskfile common tasks (#33)

Detected PolicyStack as Python-first and aligned the Taskfile build/test/lint/clean targets with the repository governance validation surface.

Co-authored-by: Codex <noreply@openai.com>

* Harden Taskfile common tasks (#34)

Co-authored-by: Codex <noreply@openai.com>

* Refine Taskfile language detection (#35)

Detect Python from uv.lock and detect Node projects from common lockfiles while continuing to prefer primary repo manifests over secondary docs tooling.

Co-authored-by: Codex <noreply@openai.com>

* Refine Taskfile clean cache coverage (#36)

Co-authored-by: Codex <noreply@openai.com>

* Refine Taskfile clean artifacts (#37)

Co-authored-by: Codex <noreply@openai.com>

* Refine Taskfile clean coverage (#38)

Include nested docs dependencies in the common clean task so Taskfile cleanup covers the repo's secondary docs package.

Co-authored-by: Codex <noreply@openai.com>

* Refine Taskfile clean coverage (#39)

Include nested docs dependencies in the common clean task so Taskfile cleanup covers the repo's secondary docs package.

Co-authored-by: Codex <noreply@openai.com>

* docs: add PR template (#40)

* ci: add trufflehog secrets scanning (#42)

* chore: pin actions to immutable SHA

* ci: expand pytest to full test suite + ruff lint gate

- Replace single-file smoke test run with full `pytest tests/ -q --tb=short`
- Add `ruff check .` and `ruff format --check .` gates
- Consolidate pip install into one step for ruff + pytest

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* chore: pin all GitHub Actions to commit SHAs

Pins all GitHub Actions to immutable commit SHAs.

* ci: add trufflehog secrets scanning

---------

Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>

* chore: pin all GitHub Actions to commit SHAs (#41)

* chore: pin actions to immutable SHA

* ci: expand pytest to full test suite + ruff lint gate

- Replace single-file smoke test run with full `pytest tests/ -q --tb=short`
- Add `ruff check .` and `ruff format --check .` gates
- Consolidate pip install into one step for ruff + pytest

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* chore: pin all GitHub Actions to commit SHAs

Pins all GitHub Actions to immutable commit SHAs.

---------

Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>

* chore: pin all GitHub Actions to commit SHAs (#41) (#43)

* chore: pin actions to immutable SHA

* ci: expand pytest to full test suite + ruff lint gate

- Replace single-file smoke test run with full `pytest tests/ -q --tb=short`
- Add `ruff check .` and `ruff format --check .` gates
- Consolidate pip install into one step for ruff + pytest



* chore: pin all GitHub Actions to commit SHAs

Pins all GitHub Actions to immutable commit SHAs.

---------

Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>

* docs: add journey-traceability + iconography implementation (#44)

Co-authored-by: Phenotype Agent <agent@phenotype.ai>

* fix(PolicyStack): add missing closing parens on lines 60-61

Both stall_count and breach_count calls were missing one ) to close int(_num(...))

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* ci: SHA-pin GitHub Actions (normalize to canonical SHAs)

Pin all action refs to immutable SHAs across workflow files:
- checkout@v4 → @11bd71901bbe5b1630ceea73d27597364c9af683
- checkout@v6 → @de0fac2e4500dabe0009e67214ff5f5447ce83dd
- setup-node@v4/v5, setup-python@v4/v5, setup-go@v5
- upload-artifact@v4/v7, download-artifact@v4
- cache@v3/v4, github-script@v7
- configure-pages@v5/v6, deploy-pages@v4/v5
- upload-pages-artifact@v3/v5, dependency-review-action@v4

Fixes version-tag normalization (add v4/v5 tags where missing).
Fixes double-SHA corruption artifacts from prior patching rounds.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* lint(PolicyStack): autofix F401, COM812, I001, format ruff --fix

705 errors auto-fixed via ruff --fix and ruff format:
- F401: removed unused imports (ASK_MODE_REVIEW, delegate/config_loader fns)
- COM812: trailing commas added throughout
- I001/I002: import blocks sorted/formatted
- RUF022: __all__ sorted
- T201/T204: print statements replaced with logging

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* fix(PolicyStack): apply --unsafe-fixes (1085 auto-fixes applied)

Resolves all F401 (unused import), T201 (bare print), I001 (sort),
COM812 (trailing comma), RUF022 (__all__ sort) in cli/ and tests/.

Remaining 51 errors: pre-existing style/complexity only.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* chore(security): bootstrap deny.toml (#46)

* chore: remove policystack README stub prior to subtree merge

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Codex <noreply@openai.com>
Co-authored-by: Koosha Paridehpour <koosha@phenotype.ai>
Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
Co-authored-by: Claude Code <claude@anthropic.com>
Co-authored-by: Codex <codex@phenotype.dev>
Co-authored-by: Forge <forge@phenotype.dev>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Koosha Pari <koosha@phenotype.space>
Co-authored-by: Phenotype Agent <agent@phenotype.ai>
@KooshaPari KooshaPari added the pr-created PR has been created and is tracked label Jun 9, 2026
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