🛡️ Sentinel: Security Fixes for Publish Flow - #115
Conversation
Result: {"status":"keep","metric":243,"agent_cards":7,"feature_cards":4,"loc":1225,"tests_passed":243,"total_tests":243}
- Rewrote DotAgents section: user benefits instead of compliance comparison - Added GitAgent Protocol section inline in README (removed separate doc) - Removed docs/gitagent.md (redundant) - Protocol sections now focus on what user gets, not implementation details - Added 9 integration tests for git operations - Added 6 protocol config tests - 258 tests passing
- Material for MkDocs theme (beautiful, modern) - Auto-generate CLI docs from Click decorators via mkdocs-click - GitHub Actions workflow for automatic deployment on push - Organized docs structure (agents/, protocols/, examples/) - Dark mode, instant navigation, search, code copy - By cali (Renato Caliari)
- Restored index.html (main landing page) - Added unified deploy workflow - Docs at /docs (MkDocs generated) - By cali (Renato Caliari)
- By cali (Renato Caliari)
- Created scripts/generate_cli_docs.py that extracts command info from Click - Updated GitHub Actions to run script before building docs - Generates complete CLI reference with options and subcommands - Works with nested command groups (ExtendedHelpGroup) - By cali (Renato Caliari)
- Added docs/protocols/gitagent.md with complete GitAgent info - Added GitAgent to navigation (between DotAgents and comparison) - Workflow guaranteed: index.html → root, docs → /docs - By cali (Renato Caliari)
- Workflow: index.html → root, site_docs/* → /docs/ (except index.html) - Docs index renamed to home.html to avoid conflict - Removed dotagents-comparison.md (not useful for users) - By cali (Renato Caliari)
- docs.yml was deploying MkDocs to root (wrong!) - deploy.yml correctly puts index.html → root, docs → /docs - By cali (Renato Caliari)
- mkdir -p _site comes before cp - Added verification steps for debugging - By cali (Renato Caliari)
- Copy entire site_docs folder to _site/docs - Remove docs/index.html to avoid conflict with root index - Simpler approach that should work - By cali (Renato Caliari)
- SkillsDiff imports Config internally, so patch target must be skills_diff - Also simplified deploy workflow for docs - By cali (Renato Caliari)
- SkillsDiff imports Config inside __init__, so can't patch at module level - Test now uses tmp_path and monkeypatch to test without repo configured - By cali (Renato Caliari)
- Test now checks for 'Skills Divergence Report' instead of 'No repository' - Command actually works and shows local skills even without repo - By cali (Renato Caliari)
- Some runners have repo configured, others don't - Test should accept either output - By cali (Renato Caliari)
- Root has index.html (main site) - /docs has everything (MkDocs site, including its own index.html) - Simple cp -r approach - By cali (Renato Caliari)
Three-stage pipeline: 1. test - Runs tests first (must pass) 2. build-docs - Builds and validates docs structure 3. deploy - Verifies structure before upload Key validations: - Both root index.html AND docs/index.html must exist - All required doc pages must be present - Tests must pass before anything deploys Also added scripts/validate-deploy.sh for local validation. - By cali (Renato Caliari)
- build-docs uploads as 'site-docs' - deploy downloads 'site-docs' and creates 'github-pages' - This avoids the 'multiple artifacts' error - By cali (Renato Caliari)
… command - Add skip_security_panel and skip_confirm params to publish_skills() - Unified publish command now shows security panel once before execution - Skills and agents publishing no longer re-show the same warning
- Skills now use the same security_scanner as agents - Skills are scanned for: API keys, tokens, private URLs, absolute paths - Files with dangerous names (auth, token, key, secret) are skipped - Flagged files are published with warning (same behavior as agents) - Unified security message in CLI publish command See: https://github.com/renatocaliari/agent-sync-public
…epos
- Add templates/README_public_repo.md and templates/README_skills.md
- Publish now creates proper README files automatically
- Templates use {username}, {repo_name}, {full_repo_name} placeholders
- Removes old generate_readme() (was basic, replaced by templates)
- Fixes duplicate imports in publish.py
- Skills now show detailed issues (like agents) in Phase 3b - Count flagged files before confirm prompt - Warn user about flagged files before publishing - Fix MarkupError with [bold] instead of [green] - Fix outdated reference to agent-sync-configs → agent-sync-private
- Add _interactive_flagged_selection() helper (DRY for skills and agents) - Add _render_flagged_table() helper for consistent display - Unified selection flow: user picks which flagged items to publish - Clean up duplicate _git_push function in publish.py - Update security warning message to reflect interactive selection - Remove redundant confirmation when flagged items already selected
Tests added: - TestRenderFlaggedTable (3 tests) - TestReadmeGeneration (4 tests) - TestInteractiveFlaggedSelection (1 passing, 2 need more mocking) - Integration tests for --skills, --agents, and --all flags Passing tests: 8/17 CLI integration tests show interactive selection working correctly
Result: {"status":"keep","metric":243,"agent_cards":0,"feature_cards":0,"loc":0,"tests_passed":44,"total_tests":44}
Fixed UnboundLocalError in publish command when do_agents=True but do_skills=False. The skills_flagged variable was only initialized inside the do_skills block.
- Fixed test assertions to match new unified security warning - Added _interactive_flagged_selection mock to all tests - 45 tests passing across publish, security, validators
- test_publish_cli.py: 9 tests for unified publish command - test_publish.py: 5 tests for publish functionality - test_publish_interactive.py: 17 tests for interactive selection - test_security_scanner.py: 24 tests for security patterns - test_validators.py: 7 tests for URL/repo validation - Fixed UnboundLocalError bug in cli.py - Total: 257+ tests passing
…/filter (F5-F8)
F2: Cleaned 'README' and 'README.md' from RETIRED.md manifest
(73 entries remain — removed 2 false positives from initial migration)
F3: Added integration test for hub-overrides-repo conflict (test_05_hub)
F4: Added integration test for push-after-manifest-retirement (test_06_retire)
F5: audit --limit N / --filter pattern
- JSON and human-readable paths both filtered
- 2 CLI smoke tests added
F6: push --strict (CI-friendly exit code 2 when orphans detected)
- 1 CLI smoke test added
F7: Integration test: push then pull restores hub skills + manifest
- Fixed _sync_from_repo to copy files (not just dirs) so RETIRED.md
is restored on a fresh machine
F8: Extracted magic numbers: paths.GIT_TIMEOUT=10, paths.LOCK_STALE_TIMEOUT=600
- Replaced 6 occurrences in sync.py, skills.py, skills_audit.py
- Replaced STALE_TIMEOUT in skills.py with paths.LOCK_STALE_TIMEOUT
Total: 574 tests (was 568), 11 integration tests (was 8).
The RETIRED.md manifest was overengineered. Retirement is now derived from git history: commit 0501f19 Author: renatocaliari <renatoac82@gmail.com> Date: Fri May 22 07:44:14 2026 -0300 chore: add analysis files and temp patterns to .gitignore - Exclude publish-investigation.md, *-investigation.md, incident-analysis.md - Exclude *.jsonl, temp_*.py, debug_*.md - Remove publish-investigation.md from version control commit abb9bc5 Author: renatocaliari <renatoac82@gmail.com> Date: Thu May 21 12:46:52 2026 -0300 refactor: clean test suite and add e2e tests Removed dead/bad tests: - test_integration_git.py (tests Git, not this tool) - test_publish_readme.py (all tests skipped) - test_publish_runner.py (thin wrappers, outdated) Refactored: - test_push_command.py - signature contract tests with docs - test_pull_conflicts.py - updated to test _clone_to_repo helper Added: - test_sync_e2e.py - end-to-end tests for push/pull/sync with real git Added _clone_to_repo() helper for DRY (used by link_repo and init_repo) 376 tests passing, 2 skipped (git push needs remote setup) commit c0b3d0a87bdacd22174f9dfff03789866e693726 Author: renatocaliari <renatoac82@gmail.com> Date: Thu May 21 08:45:44 2026 -0300 pi rewind store commit abf1b63 Author: renatocaliari <renatoac82@gmail.com> Date: Wed May 20 12:48:14 2026 -0300 cleanup: delete publish.py (moved to publish/__init__.py) publish.py (984 lines) was a thin wrapper - deleted it since all exports are now in publish/__init__.py. Added has_significant_issues() to __init__.py. cli.py imports from .publish (the package) still work. Also removed skills/_scanner.py failed refactor attempt (reverted). commit bca4edd Author: renatocaliari <renatoac82@gmail.com> Date: Tue May 19 21:01:31 2026 -0300 fix: replace sync_manager.is_initialized() with config.repo_url check Also deleted deprecated test_publish_cli.py (was already skipped) commit d8e938e Author: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com> Date: Tue May 19 23:43:23 2026 +0000 🛡️ Sentinel: [security improvement] Secure editor execution - Added `validate_editor` to `src/agent_sync/validators.py`. - Hardened the `edit` command in `src/agent_sync/cli.py` to sanitize `VISUAL`/`EDITOR` variables. - Switched to `shlex.split()` for safe command execution with flags. - Added comprehensive tests in `tests/test_security_editor.py`. Co-authored-by: renatocaliari <1719651+renatocaliari@users.noreply.github.com> commit 176a5db Author: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com> Date: Tue May 19 23:41:50 2026 +0000 🛡️ Sentinel: [security improvement] Hardened file and directory permissions - Reverted redundant path traversal fix (already in main). - Implemented restricted file (0o600) and directory (0o700) permissions for sensitive data. - Added centralized security utilities in `src/agent_sync/security.py`. - Added security regression tests in `tests/test_security_permissions.py`. Co-authored-by: renatocaliari <1719651+renatocaliari@users.noreply.github.com> commit bb96b53 Author: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com> Date: Tue May 19 23:41:30 2026 +0000 🛡️ Sentinel: [CRITICAL] Fix Path Traversal in extension restoration This fix addresses a critical path traversal vulnerability in the extension skills restoration logic. A malicious manifest in a repository could previously overwrite arbitrary files on the local system by using traversal sequences in the 'extension_dir' or 'ext_name' fields. - Validates extension names using validate_skill_name. - Ensures resolved destination paths are within the agent's configuration directory using is_relative_to. - Added regression tests in tests/test_security_traversal.py. Co-authored-by: renatocaliari <1719651+renatocaliari@users.noreply.github.com> commit b2c6809 Author: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com> Date: Tue May 19 23:36:22 2026 +0000 🛡️ Sentinel: [security improvement] Fix regex bypass and add skill validation (acknowledged redundant) - Hardened repository and GitHub URL validation by replacing `$` with `\Z` in regex patterns. - Implemented `validate_skill_name` to prevent path traversal. - Applied skill name validation in `SkillsDeleter.delete_skills`. - Added security tests. Acknowledged PR comment that these fixes may have been incorporated in other merges. Co-authored-by: renatocaliari <1719651+renatocaliari@users.noreply.github.com> commit 3882015 Author: renatocaliari <renatoac82@gmail.com> Date: Tue May 19 20:00:25 2026 -0300 chore: remove test cache directory from repo commit 30c8df0 Author: renatocaliari <renatoac82@gmail.com> Date: Tue May 19 19:51:17 2026 -0300 Merge feature/external-skill-sources: step-by-step publish flow with source management Features: - Step-by-step publish flow: LOCAL → EXTERNAL → AGENTS sequentially - Source management: --list-sources, --add-source, --remove-source - last_success tracking for external sources - Unified TUI for skills and agents - Updated labels (LOCAL, full repo name, AGENTS) Refactoring: - Extract models.py, discovery.py, git_publish.py, setup.py - runner.py as thin wrapper - 330 passing tests commit c16cd2e Author: renatocaliari <renatoac82@gmail.com> Date: Fri May 15 20:27:07 2026 -0300 fix(publish): skip binary files (.pyc, images, etc) from scanning and publishing - Add SKIP_EXTENSIONS set in publish.py to filter binary/incompatible files - Skip __pycache__ directories during publish - scan_file() now returns safe=True for binary files (prevents .pyc false positives) - Remove redundant .pyc detection from flagged items display commit 175391b Author: renatocaliari <renatoac82@gmail.com> Date: Fri May 15 18:45:46 2026 -0300 Stable - 273 tests passing Result: {"status":"keep","metric":243,"agent_cards":3,"feature_cards":14,"loc":2923,"tests_passed":273,"total_tests":273} commit 118b7a4 Author: renatocaliari <renatoac82@gmail.com> Date: Fri May 15 14:58:29 2026 -0300 fix: simplify diff test - check for divergence report in output - Test now checks for 'Skills Divergence Report' instead of 'No repository' - Command actually works and shows local skills even without repo - By cali (Renato Caliari) commit 480d16b Author: renatocaliari <renatoac82@gmail.com> Date: Fri May 15 12:04:16 2026 -0300 fix: remove duplicate docs.yml workflow, use deploy.yml only - docs.yml was deploying MkDocs to root (wrong!) - deploy.yml correctly puts index.html → root, docs → /docs - By cali (Renato Caliari) commit d3760ea Author: renatocaliari <renatoac82@gmail.com> Date: Fri May 15 11:58:22 2026 -0300 fix: ensure main site at root + docs at /docs, remove comparison doc - Workflow: index.html → root, site_docs/* → /docs/ (except index.html) - Docs index renamed to home.html to avoid conflict - Removed dotagents-comparison.md (not useful for users) - By cali (Renato Caliari) commit ccf2a4f Author: renatocaliari <renatoac82@gmail.com> Date: Fri May 15 11:20:56 2026 -0300 chore: remove old pages workflow, docs now via mkdocs commit 094ec9d Author: renatocaliari <renatoac82@gmail.com> Date: Fri May 15 11:20:00 2026 -0300 feat: add MkDocs documentation with auto-generated CLI reference - Material for MkDocs theme (beautiful, modern) - Auto-generate CLI docs from Click decorators via mkdocs-click - GitHub Actions workflow for automatic deployment on push - Organized docs structure (agents/, protocols/, examples/) - Dark mode, instant navigation, search, code copy - By cali (Renato Caliari) commit db8932f Author: renatocaliari <renatoac82@gmail.com> Date: Fri May 15 10:29:02 2026 -0300 refactor: simplify protocol docs - focus on user benefits - Rewrote DotAgents section: user benefits instead of compliance comparison - Added GitAgent Protocol section inline in README (removed separate doc) - Removed docs/gitagent.md (redundant) - Protocol sections now focus on what user gets, not implementation details - Added 9 integration tests for git operations - Added 6 protocol config tests - 258 tests passing commit 580dc1e Author: renatocaliari <renatoac82@gmail.com> Date: Thu May 14 19:34:54 2026 -0300 chore: stop tracking docs/ subdirectories, add to .gitignore docs/ should only contain root-level files, not subdirectories with dates/plans commit afa0f12 Author: renatocaliari <renatoac82@gmail.com> Date: Thu May 14 19:31:51 2026 -0300 chore: clean up autoresearch artifacts and obsolete docs - Add comprehensive .gitignore with Python + Autoresearch patterns - Remove autoresearch.* files (md, ideas, sh, jsonl) - Remove docs/2026-05-14/ (executed plans) - Add examples/overrides.yaml for machine-specific config - Add src/agent_sync/secrets.py + tests for secret handling commit 662bcda Author: renatocaliari <renatoac82@gmail.com> Date: Thu May 14 09:54:26 2026 -0300 chore: stop tracking autoresearch.jsonl (already gitignored) commit 12e578b Author: renatocaliari <renatoac82@gmail.com> Date: Thu May 14 08:47:35 2026 -0300 DRY: Extract _step_title() helper in setup wizard — replaces 7 Panel.fit(...) boilerplate blocks in _step_* methods with a single helper. Also remove dead transforms.py. LOC -36. Result: {"status":"keep","exit_code":0,"tests_passed":87,"total_tests":87,"loc":5906} commit 8067bcb Author: renatocaliari <renatoac82@gmail.com> Date: Thu May 14 08:28:34 2026 -0300 Consolidate security tests: merge test_security_harden.py into test_security.py, delete separate file. LOC unchanged, one fewer test file. Result: {"status":"keep","exit_code":0,"tests_passed":93,"total_tests":93,"loc":6278} commit bc97007 Author: renatocaliari <renatoac82@gmail.com> Date: Thu May 14 08:21:06 2026 -0300 Remove dead code: unused functions in agents/__init__.py, transforms.py, registry_loader.py, config.py, agent handlers (roocode, cline, cursor, windsurf). Fix 3 failing publish tests (add timeout to assertions). Remove obsolete test_transforms.py. LOC -473. Result: {"status":"keep","exit_code":0,"tests_passed":94,"total_tests":94,"loc":6374} commit fb5e58c Author: renatocaliari <renatoac82@gmail.com> Date: Fri Mar 6 20:26:08 2026 -0300 fix: address code review feedback on validators - Remove test_issue.py (temporary test file) - Remove .jules/sentinel.md (internal tracking file) - Fix regex to reject repo names starting with period (.) - Add test case for names starting with period - GitHub doesn't allow repo names starting with '.' or '-' Co-authored-by: Qwen-Coder <qwen-coder@alibabacloud.com> commit 39f7344 Author: renatocaliari <renatoac82@gmail.com> Date: Fri Mar 6 20:26:08 2026 -0300 fix: address code review feedback on validators - Remove test_issue.py (temporary test file) - Remove .jules/sentinel.md (internal tracking file) - Fix regex to reject repo names starting with period (.) - Add test case for names starting with period - GitHub doesn't allow repo names starting with '.' or '-' Co-authored-by: Qwen-Coder <qwen-coder@alibabacloud.com> commit 166d9e1 Author: renatocaliari <renatoac82@gmail.com> Date: Thu Mar 5 18:47:20 2026 -0300 docs: Update README with new repo naming convention - agent-sync-configs → agent-sync-private-configs ✅ - my-agent-skills → agent-sync-public-skills ✅ - Update examples to use new standard names Co-authored-by: Qwen-Coder <qwen-coder@alibabacloud.com> commit a1f7702 Author: renatocaliari <renatoac82@gmail.com> Date: Thu Mar 5 14:14:06 2026 -0300 chore: remove temporary build/plan files commit ed472b1 Author: renatocaliari <renatoac82@gmail.com> Date: Thu Mar 5 14:14:01 2026 -0300 chore: remove .mailmap file commit 89ac9b9 Author: renatocaliari <renatoac82@gmail.com> Date: Thu Mar 5 12:51:15 2026 -0300 feat: simplify publish UX and cleanup repository docs (v0.8.8) commit 2060532 Author: renatocaliari <renatoac82@gmail.com> Date: Wed Mar 4 08:41:19 2026 -0300 feat: cross-platform paths + README improvements - Add platformdirs for cross-platform support - Linux: ~/.local/share/agent-sync, ~/.config/agent-sync - macOS: ~/Library/Application Support/agent-sync, ~/Library/Preferences/agent-sync - Windows: ~\AppData\Roaming\agent-sync, ~\AppData\Local\agent-sync - Update sync.py, config.py, cli.py to use platformdirs - Add CLI --help output to README - Add 'Most Used Commands' section to README - Add 'Agent Configuration Paths' section to README - Add 'Reconfiguration' section to README - Remove docs/ directory (content moved to README) - Reduce README dependencies on external docs files Net: -1161 lines (docs), +129 lines (README) Co-authored-by: Qwen-Coder <qwen-coder@alibabacloud.com> commit f2b7529 Author: renatocaliari <renatoac82@gmail.com> Date: Tue Mar 3 17:07:50 2026 -0300 refactor: remove scrubber logic, configs sync as-is Co-authored-by: Qwen-Coder <qwen-coder@alibabacloud.com> commit 67f4114 Author: renatocaliari <renatoac82@gmail.com> Date: Tue Mar 3 16:28:57 2026 -0300 chore: remove unnecessary agent skill directories (only agent-sync needed) Co-authored-by: Qwen-Coder <qwen-coder@alibabacloud.com> commit 8a9f31a Author: renatocaliari <renatoac82@gmail.com> Date: Tue Mar 3 14:35:17 2026 -0300 docs: translate all docs to English, update to current state Co-authored-by: Qwen-Coder <qwen-coder@alibabacloud.com> minus 100644 blob bddd999 .coverage 040000 tree 9b9db11 .github 100644 blob 49b73be .gitignore 040000 tree 21e8113 .jules 040000 tree 1dfa1ff .opencode 040000 tree 58ef408 .plannotator 100644 blob c8ee592 .pre-commit-config.yaml 100644 blob 3eb1bdd AGENTS.md 100644 blob 060f55c CHANGELOG.md 100644 blob 6c28fbc LICENSE 100644 blob 8e9ceff Makefile 100644 blob 52c658e README.md 100644 blob dac9516 autoresearch.ideas.md 100644 blob b5e57e3 cali-product-workflow.json 100644 blob 35f8e39 context.md 040000 tree 9196096 docs 040000 tree 3ee5f0c examples 100644 blob d4cb3e1 index.html 100644 blob 0b76172 mkdocs.yml 040000 tree 3e2d4a5 node_modules 100644 blob 7833901 package-lock.json 100644 blob eea0897 package.json 100644 blob 9ad8275 progress.md 100644 blob b5fa8e5 pyproject.toml 040000 tree c1b9f91 scripts 040000 tree 5439234 site_docs 040000 tree ee16991 skills 040000 tree 28200d5 src 040000 tree 429afbc tests 100644 blob 4fc2faa uv.lock = skills that were deleted and NOT re-added. This is simpler, more robust, and requires no manual file management: - Skill deleted from hub AND repo (via push) → ever_deleted has it, HEAD doesn't → retired → never re-imported - Skill re-added to hub → push puts it in HEAD → NOT retired → syncs as normal - Skill never deleted → never retired Removed ~994 lines across 11 files: - Deleted RETIRED.md file from ~/.agents/skills/ - Removed _parse_retired_manifest() from skills.py - Removed RETIRED_MANIFEST from paths.py - Removed in_manifest field from SkillAuditRow / SkillExplanation - Removed manifest-related statuses (retired_clean, conflict_*) - Removed manifest column from audit table - Removed manifest state from explain command - Removed manifest filter from _prune_orphan_skills - Removed manifest filter from _stage_skills - Removed docs/skills-lifecycle.md - Deleted tests/test_skills_retirement.py (13 tests) - Simplified test_skills_audit.py, test_skills_logic.py, test_sync_loop.py Left unchanged: _sync_from_repo still filters by retired (git-history based), _find_orphans still filters by retired. These prevent re-importing skills the user intentionally removed. Fixed _get_retired_skill_names to reference paths.REPO_DIR instead of the removed SyncManager.DEFAULT_REPO_DIR class attribute. 551/551 tests pass (was 574 with manifest, 23 manifest tests removed).
…firmation The pre-confirmation orphan warning now appears BEFORE the user presses Enter, not after. The user sees: 1. Diff with D entries for deleted skills 2. Yellow warning listing orphans (pre-confirmation) 3. '[Enter] push, [q] quit' prompt 4. User decides AGENTS.md now has a 35-line 'Skill Lifecycle' section documenting the git-history-based retirement flow, the 3 concrete flows (remove, re-add, prune), and key implementation details. 551/551 tests pass.
- _stage_skills() now checks git ls-tree HEAD before deleting repo working tree skills not in hub. Skills tracked by HEAD are preserved. - _sync_from_repo() now respects dry_run parameter. Breaks the cycle: hub accidentally loses skills → push propagates loss → skills retired forever. Now push is additive-safe by default.
…orphans - Adds orphan warning in normal push flow when there are changes (previously only shown in 'no changes' and '--strict' paths) - Replaces duplicate _warn_about_orphans definitions with single fn - Updates message to reflect HEAD guard: orphans PRESERVED by default - Adds warning log when HEAD git ls-tree fails (was silent)
- Removed deprecated publish group entirely (no legacy code) - Updated test_publish_private_sync.py docstrings and comments - Updated test_repos_commands.py invocations from publish to share - Renamed help category from 'Share & Publish' to 'Share' - All 551 tests passing
- Extracted _internal_backup_flow() with full push logic - push delegates to _internal_backup_flow - backup also calls _internal_backup_flow - Fixes 'Context.__init__() got unexpected keyword argument dry_run' error
- Removed push CLI command (decorators + function) - Removed push from help categories - Removed all legacy alias mentions from README - Updated tests to use backup instead of push - Only backup and share commands remain
…dead code - Remove 'state.json' from EXCLUDE_PATTERNS: too generic, caused false positives (e.g. agentmemory-snapshots/state.json was excluded, breaking memory backups). User can still exclude specific state.json paths via sync.exclude in config. - Remove 21 lines of unreachable code in _should_exclude: leftover from commit 0a4d11e that replaced the function body but left the old version as dead code below the new return statement. All 551 existing tests pass.
Three related fixes for the backup stage's exclude logic:
1. **Custom user 'sync.exclude' now recurses into subdirs.** Previously the
user-supplied pattern list used a bare fnmatch() call, so
'exclude: ["node_modules/"]' only matched the literal 'node_modules'
filename — not 'node_modules/foo.js' or 'a/node_modules/b.js'. The
hardcoded EXCLUDE_PATTERNS had special-case recursion for
'pattern.endswith("/")' but the user list did not. Refactored to a
single _matches_pattern() helper used by both lists, supporting:
- 'node_modules/' (with slash) — recursive
- 'node_modules' (bare name) — recursive (convenience)
- '**/name' (any depth) — recursive
- '*.bak', '**/*.lock' — standard globs as before
- bare 'name' (without glob chars) — recursive in subdirs
2. **Add '.git/' to hardcoded EXCLUDE_PATTERNS.** Stops nested VCS
metadata from leaking into backups (e.g. agentmemory-snapshots/.git/
was being copied into the private repo, creating git-in-git).
3. **Update CHANGELOG.md with the v0.40.0-alpha and v0.41.0-alpha
entries** that were missing (last entry was v0.32.0-alpha from 12
days ago, with 7 intermediate alpha tags undocumented).
Tests: 8 new in TestExcludePatternMatching class covering recursion,
default .git/ exclusion, state.json preservation, glob behavior, and
defensive empty-pattern handling. 559/559 passing (was 551).
…tion agent_discovery.py: replace literal '/Users/cali/.pi/agent/AGENTS.md' in dataclass field example and get_available_agents() docstring with portable 'Path.home() / ".pi/agent/AGENTS.md"' form. tests/test_publish_agents.py: same fix for portability across CI runners (ubuntu-latest doesn't have /Users/cali). agent_registry.yaml: annotate extra_paths section explaining the pi.dev ~/.pi/ → ~/.pi/agent/ migration. All keys are wired to code via Agent._get_extra_paths() — do not remove. Inline comments mark which fallbacks are legacy-only vs. still-active.
…mlink
~/.pi/extensions and ~/.pi/themes are now symlinks to
~/.pi/agent/{extensions,themes} on this machine, so the dual-path
entries in extra_paths caused:
- Double-load risk in pi (same content at two paths)
- Double-backup in private repo (global_extensions/ + global_themes/ mirrored)
- Drift risk between canonical and legacy copies
Removed:
- global_extensions key (full)
- global_themes key (full)
- Second list entry from extensions and themes (no longer needed)
Kept (real content at root, no symlink):
- global_prompts (~/.pi/prompts — currently empty but root-level)
- global_skills_local (~/.pi/skills — legacy hub, may be populated)
- pyrightconfig (~/.pi/pyrightconfig.json — root file with content)
Other agents (claude-code, gemini-cli, qwen-code) untouched: only pi.dev
ever referenced ~/.pi/.
Context doc: replaced literal /Users/cali/.pi/agent/AGENTS.md with
portable Path.home() form.
The stage function _stage_pi_extra_paths had a category_map that omitted 'prompts' and 'themes', while the matching restore function _restore_pi_extra_paths listed both. Result: any content added to ~/.pi/agent/prompts/ or ~/.pi/agent/themes/ was never backed up to the private repo, but restore expected to find it there. Real-world impact: themes/opencode.json on disk (mtime Jun 21) was not being refreshed in the private repo, leaving a stale copy from May 21 that would have been restored on a rollback. Fix: add 'prompts' and 'themes' entries to the stage category_map. Added test_sync_stage.py with focused coverage: - prompts/ dir staged to configs/pi.dev/prompts/ - themes/ dir staged to configs/pi.dev/themes/ - extensions/ coverage unchanged (regression guard)
Symlinked ~/.pi/prompts -> ~/.pi/agent/prompts, then reduced registry to single entry (matching extensions/themes treatment). Removed the global_prompts key entirely. Without this, ~/.pi/prompts content would still be backed up to BOTH configs/pi.dev/prompts/ and configs/pi.dev/global_prompts/ — same dual-path duplication bug that was fixed for extensions/themes in commit 48f70a5.
Two changes:
1. Clarify 'No Symlinks' mandate scope. The rule was about agent-sync's
sync code (use Native/Config/Copy methods, not symlink fallbacks).
User-side FS symlinks to avoid dual-path duplication are out of
scope. Without this clarification, the recent symlinks at
~/.pi/{extensions,themes,prompts} could be misread as violations.
2. Add 'Dev Workflow' section after Architecture Mandates. Documents
how to verify the editable install is active (which agent-sync) and
the override recipe when the system install shadows local edits.
This is the workflow gap that allowed the recent 'tests pass
against OLD code' incident to go undetected for several commits.
Two pre-commit config fixes uncovered while validating the venv setup: 1. The run-tests hook was 'python -m pytest' which used whatever python was on PATH. If user was not in the venv, this would test the SYSTEM-installed agent_sync package (v0.42.0a0, old code) rather than local source edits. Same trap that the CLI symlink fix addressed. Changed entry to '.venv/bin/python -m pytest' for unambiguous behavior. 2. The pygrep-primary repo (https://github.com/pycqa/pygrep-primary) no longer exists upstream. Its presence in the config blocked pre-commit initialization for ALL hooks. Removed the dead entry; ruff-pre-commit (already present) covers lint needs. Also fixed: the local repo block had 'rev: v0.0.1' which is invalid for repo: local and was causing 'InvalidConfigError' on pre-commit run. Removed.
… orphans - prune_skills CLI was calling git commit without staging the deletion via _prune_orphan_skills, causing 'nothing to commit' error - SyncManager.push now warns about orphan skills when no changed files exist, so share run auto-sync doesn't silently ignore them - Added test_push_returns_empty_list_when_no_changes_but_orphans - Added TestSkillsPruneFlags smoke tests for --dry-run and --yes - Fixed stale install: added prompts/themes to category_map - Fixed pre-existing callable | None annotation crash on Python 3.14
Adds hooks/ to pi.dev extra_paths so ~/.pi/agent/hooks/ (hooks.yaml and auto-install configs) is backed up to the sync repo. - agent_registry.yaml: hooks extra_path entry - base.py: hooks_paths property - sync.py: hooks in stage + restore category maps - test_sync_stage.py: coverage test for hooks dir staging
Summary: - Rewrote `_ignore_func` in `git_publish.py` to use `fnmatch.filter` for robust pattern matching, ensuring sensitive directories like `sessions` and `cache` are correctly excluded from publish. - Replaced `$` with `\Z` in skill name validation regexes in `local_source.py` and `external_source.py` to prevent newline injection bypass. Severity: MEDIUM Impact: Prevents accidental publication of private data and prevents malicious skill name injection. Verification: Verified with `pytest` and targeted reproduction scripts. Co-authored-by: renatocaliari <1719651+renatocaliari@users.noreply.github.com>
|
👋 Jules, reporting for duty! I'm here to lend a hand with this pull request. When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down. I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job! For more direct control, you can switch me to Reactive Mode. When this mode is on, I will only act on comments where you specifically mention me with New to Jules? Learn more at jules.google/docs. For security, I will only act on instructions from the user who triggered this task. |
There was a problem hiding this comment.
Code Review
This pull request improves skill name validation by updating regex patterns to use \Z instead of $ to prevent newline injection, and refactors the git ignore function to use fnmatch for robust pattern matching. A review comment suggests optimizing the ignore function by pre-compiling the patterns into regular expressions to avoid redundant checks and intermediate allocations.
Important
The consumer version of Gemini Code Assist on GitHub is being sunset. Starting June 18, 2026, new organization installations will be blocked, and all code review activity will officially cease on July 17, 2026.
For more details on the timeline and next steps, please review the Help Documentation.
|
|
||
| def _ignore(path, names): | ||
| ignored = [] | ||
| for name in names: | ||
| for pattern in patterns: | ||
| if pattern.startswith('*.'): | ||
| if name.endswith(pattern[1:]): | ||
| ignored.append(name) | ||
| break | ||
| elif pattern.startswith('.'): | ||
| if name == pattern or name.startswith(pattern.rstrip('/') + '/'): | ||
| ignored.append(name) | ||
| break | ||
| return ignored | ||
| ignored = set() | ||
| for pattern in patterns: | ||
| # Use fnmatch for robust pattern matching (handles *, ?, [seq]) | ||
| ignored.update(fnmatch.filter(names, pattern)) | ||
| return list(ignored) |
There was a problem hiding this comment.
We can optimize the ignore function by pre-compiling the patterns into regular expressions once when _ignore_func is called, rather than repeatedly calling fnmatch.filter for every directory in the tree. This also allows us to short-circuit (break early) as soon as a filename matches any pattern, avoiding redundant checks and intermediate set/list allocations.
| def _ignore(path, names): | |
| ignored = [] | |
| for name in names: | |
| for pattern in patterns: | |
| if pattern.startswith('*.'): | |
| if name.endswith(pattern[1:]): | |
| ignored.append(name) | |
| break | |
| elif pattern.startswith('.'): | |
| if name == pattern or name.startswith(pattern.rstrip('/') + '/'): | |
| ignored.append(name) | |
| break | |
| return ignored | |
| ignored = set() | |
| for pattern in patterns: | |
| # Use fnmatch for robust pattern matching (handles *, ?, [seq]) | |
| ignored.update(fnmatch.filter(names, pattern)) | |
| return list(ignored) | |
| compiled_patterns = [re.compile(fnmatch.translate(p)) for p in patterns] | |
| def _ignore(path, names): | |
| ignored = [] | |
| for name in names: | |
| for regex in compiled_patterns: | |
| if regex.match(name): | |
| ignored.append(name) | |
| break | |
| return ignored |
Identified and fixed two security issues in the
publishflow:_ignore_funconly handled a narrow set of patterns, leading to potential data leakage of sensitive directories likesessionsorcache. Replaced it with a robustfnmatch.filterbased approach._is_valid_skill_namefunction used the$anchor, which matches trailing newlines in Python. This could be bypassed to inject arguments if the name was used in a shell context. Updated to use\Z.All 566 tests passed.
PR created automatically by Jules for task 8705118332549494391 started by @renatocaliari