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chore(deps): add renovate.json5 - #35

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Apr 28, 2026
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chore(deps): add renovate.json5#35
KooshaPari merged 1 commit into
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chore/add-renovate-2026-04-27

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@KooshaPari

@KooshaPari KooshaPari commented Apr 28, 2026

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Renovate config: cargo + github-actions weekly Monday, grouped non-major updates.

Note

Low Risk
Low risk: adds only repository automation config and does not change runtime code paths. Impact is limited to how dependency update PRs are scheduled and grouped.

Overview
Adds renovate.json5 to enable Renovate with weekly (Monday, before 4am) dependency update PRs using config:base and group:allNonMajor.

Configures bump range strategy, rate limits (prHourlyLimit/prConcurrentLimit), default dependencies labeling, security-labeled vulnerability alerts, and package rules to group non-major updates for cargo and github-actions (including digests).

Reviewed by Cursor Bugbot for commit 1ed4dbc. Bugbot is set up for automated code reviews on this repo. Configure here.


CodeAnt-AI Description

Add scheduled dependency update PRs with grouped non-major updates

What Changed

  • Dependency update PRs are now created on Monday before 4am instead of at unpredictable times
  • Non-major Rust and GitHub Actions updates are grouped into fewer PRs
  • Dependency PRs now use a shared dependencies label, and security alerts get a separate security label
  • Update volume is capped so the repository is less likely to receive too many dependency PRs at once

Impact

✅ Fewer dependency update PRs
✅ Easier review of routine updates
✅ Clearer security alert tracking

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@KooshaPari
KooshaPari merged commit e4727df into main Apr 28, 2026
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KooshaPari deleted the chore/add-renovate-2026-04-27 branch April 28, 2026 01:58
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Run ID: c1ad0478-e4f1-4265-a804-c422b1d937d3

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📒 Files selected for processing (1)
  • renovate.json5
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@codeant-ai codeant-ai Bot added the size:S This PR changes 10-29 lines, ignoring generated files label Apr 28, 2026

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Cursor Bugbot has reviewed your changes and found 1 potential issue.

Fix All in Cursor

Bugbot Autofix is ON, but it could not run because the branch was deleted or merged before autofix could start.

Reviewed by Cursor Bugbot for commit 1ed4dbc. Configure here.

Comment thread renovate.json5
{
"$schema": "https://docs.renovatebot.com/renovate-schema.json",
"extends": [
"config:base",

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New config uses deprecated config:base preset name

Low Severity

This brand-new configuration file uses config:base, which was renamed to config:recommended in Renovate v36 (June 2023). While Renovate's migration code still handles the old name, a newly added config file is better off using the current canonical name to avoid relying on deprecated compatibility shims.

Fix in Cursor Fix in Web

Reviewed by Cursor Bugbot for commit 1ed4dbc. Configure here.

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@codeant-ai codeant-ai Bot added size:S This PR changes 10-29 lines, ignoring generated files and removed size:S This PR changes 10-29 lines, ignoring generated files labels May 6, 2026
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Sequence Diagram

This PR adds a Renovate configuration that runs weekly on Monday before 4am to create grouped, labeled dependency update pull requests for Rust and GitHub Actions, with separate labeling for security alerts and limits on PR volume.

sequenceDiagram
    participant Scheduler
    participant Renovate
    participant GitHost
    participant Maintainer

    Scheduler->>Renovate: Trigger weekly run before 4am Monday
    Renovate->>Renovate: Scan dependencies and security alerts
    Renovate->>Renovate: Group non major Rust and GitHub Actions updates
    Renovate->>GitHost: Create labeled dependency and security PRs
    GitHost-->>Maintainer: Notify about grouped update PRs
Loading

Generated by CodeAnt AI

Comment thread renovate.json5
Comment on lines +13 to +24
"packageRules": [
{
"matchManagers": ["cargo"],
"groupName": "rust deps (non-major)",
"matchUpdateTypes": ["minor", "patch"]
},
{
"matchManagers": ["github-actions"],
"groupName": "github-actions",
"matchUpdateTypes": ["minor", "patch", "digest"]
}
]

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Suggestion: This repository already has active Dependabot rules for both cargo and github-actions in .github/dependabot.yml, so adding Renovate for the same ecosystems will create duplicate dependency PRs and conflicting update churn. Disable one bot (or scope Renovate to non-overlapping managers) so only a single updater owns each ecosystem. [logic error]

Severity Level: Major ⚠️
- ⚠️ Duplicate cargo update PRs from Dependabot and Renovate.
- ⚠️ Duplicate GitHub Actions update PRs from both bots.
- ⚠️ Noisy dependency workflow complicates reviewer triage and merging.
Steps of Reproduction ✅
1. Push this repository to GitHub with existing Dependabot config at
`.github/dependabot.yml:1-19`, where `package-ecosystem: "cargo"` and `package-ecosystem:
"github-actions"` are both configured with their own schedules and labels.

2. Enable Renovate for the repository so that GitHub reads `renovate.json5:1-25`,
including `packageRules` at lines 13-24 that match managers `"cargo"` and
`"github-actions"` for non-major updates.

3. Allow any Rust dependency in `Cargo.toml` at the repo root to become outdated;
Dependabot (per `.github/dependabot.yml:3-10`) opens a cargo update PR, while Renovate
(per `renovate.json5:13-18`) also opens a grouped non-major cargo PR for the same outdated
packages.

4. Allow any GitHub Actions workflow in `.github/workflows/` to reference an outdated
action version; Dependabot (per `.github/dependabot.yml:12-19`) opens a `github-actions`
update PR and Renovate (per `renovate.json5:19-23`) opens a separate grouped
`github-actions` PR, resulting in duplicate automation for the same ecosystem.

Fix in Cursor | Fix in VSCode Claude

(Use Cmd/Ctrl + Click for best experience)

Prompt for AI Agent 🤖
This is a comment left during a code review.

**Path:** renovate.json5
**Line:** 13:24
**Comment:**
	*Logic Error: This repository already has active Dependabot rules for both `cargo` and `github-actions` in `.github/dependabot.yml`, so adding Renovate for the same ecosystems will create duplicate dependency PRs and conflicting update churn. Disable one bot (or scope Renovate to non-overlapping managers) so only a single updater owns each ecosystem.

Validate the correctness of the flagged issue. If correct, How can I resolve this? If you propose a fix, implement it and please make it concise.
Once fix is implemented, also check other comments on the same PR, and ask user if the user wants to fix the rest of the comments as well. if said yes, then fetch all the comments validate the correctness and implement a minimal fix
👍 | 👎

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@codeant-ai codeant-ai Bot added size:S This PR changes 10-29 lines, ignoring generated files and removed size:S This PR changes 10-29 lines, ignoring generated files labels May 6, 2026
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Sequence Diagram

This PR adds a Renovate configuration that schedules weekly dependency update checks, grouping non-major Rust and GitHub Actions updates into labeled pull requests with separate handling for security alerts.

sequenceDiagram
    participant Scheduler
    participant Renovate
    participant Repo
    participant Maintainer

    Scheduler->>Renovate: Weekly Monday trigger
    Renovate->>Repo: Scan cargo and GitHub Actions dependencies
    Renovate->>Renovate: Group non major updates for cargo and actions
    Renovate->>Repo: Create dependency PRs with dependencies label
    Renovate->>Repo: Create security PRs with security label
    Repo-->>Maintainer: Show grouped dependency and security PRs
Loading

Generated by CodeAnt AI

Comment thread renovate.json5
"group:allNonMajor",
":enableVulnerabilityAlertsWithLabel(security)"
],
"schedule": ["before 4am on monday"],

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Suggestion: The schedule is defined without a timezone, so "before 4am on monday" is interpreted in Renovate's runtime timezone (commonly UTC), which can run at the wrong local time/day versus team expectations. Add an explicit timezone to make execution deterministic. [possible bug]

Severity Level: Major ⚠️
- ⚠️ Dependency update timing tied to Renovate's default timezone.
- ⚠️ Potential mismatch with maintainers' expected local update window.
Steps of Reproduction ✅
1. Open `renovate.json5:8`, where the schedule is configured as `"schedule": ["before 4am
on monday"]` without any `"timezone"` field in this file or elsewhere in the repo (no
other Renovate config files are present).

2. According to Renovate's documented behavior (referenced by the `$schema` at line 2),
when `timezone` is omitted, the schedule is evaluated in Renovate's default timezone
(commonly UTC or the host/repo timezone), not in an explicitly defined project-local
timezone.

3. Enable the Renovate GitHub App for this repository so that it honors the `schedule` in
`renovate.json5`; dependency update PRs will then be created "before 4am on monday" in
that default timezone.

4. If the team expects "before 4am on Monday" in a specific local timezone (e.g., their
office region) rather than Renovate's default, the actual PR creation time may differ from
their local Monday/4am expectation; this behavior stems directly from the missing
`"timezone"` setting next to the `schedule` entry in `renovate.json5`.

Fix in Cursor | Fix in VSCode Claude

(Use Cmd/Ctrl + Click for best experience)

Prompt for AI Agent 🤖
This is a comment left during a code review.

**Path:** renovate.json5
**Line:** 8:8
**Comment:**
	*Possible Bug: The schedule is defined without a `timezone`, so "before 4am on monday" is interpreted in Renovate's runtime timezone (commonly UTC), which can run at the wrong local time/day versus team expectations. Add an explicit timezone to make execution deterministic.

Validate the correctness of the flagged issue. If correct, How can I resolve this? If you propose a fix, implement it and please make it concise.
Once fix is implemented, also check other comments on the same PR, and ask user if the user wants to fix the rest of the comments as well. if said yes, then fetch all the comments validate the correctness and implement a minimal fix
👍 | 👎

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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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