Codex CLI reads skills natively from ~/.agents/skills/ (installed by
ECC installer / npx skills). The sync script was redundantly copying
the same skills from .agents/skills/ to ~/.codex/skills/.
Changes:
- Remove skill copy loop, variables, and path validation from sync script
- Update sanity checker to validate ~/.agents/skills/ instead of
~/.codex/skills/, downgrade missing skills from FAIL to WARN
- Update test assertions to verify skill sync removal
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* feat: add pending instinct TTL pruning and /prune command
Pending instincts generated by the observer accumulate indefinitely
with no cleanup mechanism. This adds lifecycle management:
- `instinct-cli.py prune` — delete pending instincts older than 30 days
(configurable via --max-age). Supports --dry-run and --quiet flags.
- Enhanced `status` command — shows pending count, warns at 5+,
highlights instincts expiring within 7 days.
- `observer-loop.sh` — runs prune before each analysis cycle.
- `/prune` slash command — user-facing command for manual pruning.
Design rationale: council consensus (4/4) rejected auto-promote in
favor of TTL-based garbage collection. Frequency of observation does
not establish correctness. Unreviewed pending instincts auto-delete
after 30 days; if the pattern is real, the observer will regenerate it.
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* fix: remove duplicate functions, broaden extension filter, fix prune output
- Remove duplicate _collect_pending_dirs and _parse_created_date defs
- Use ALLOWED_INSTINCT_EXTENSIONS (.md/.yaml/.yml) instead of .md-only
- Track actually-deleted items separately from expired for accurate output
- Update README.md and AGENTS.md command counts: 59 → 60
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* fix: address Copilot and CodeRabbit review findings
- Use is_dir() instead of exists() for pending path checks
- Change > to >= for --max-age boundary (--max-age 0 now prunes all)
- Use CLV2_PYTHON_CMD env var in observer-loop.sh prune call
- Remove unused source_dupes variable
- Remove extraneous f-string prefix on static string
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* fix: update AGENTS.md project structure command count 59 → 60
Co-Authored-By: Claude <noreply@anthropic.com>
* fix: address cubic and coderabbit review findings
- Fix status early return skipping pending instinct warnings (cubic #1)
- Exclude already-expired items from expiring-soon filter (cubic #2)
- Warn on unparseable pending instinct age instead of silent skip (cubic #4)
- Log prune failures to observer.log instead of silencing (cubic #5)
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* fix: YAML single-quote unescaping, f-string cleanup, add /prune to README
- Fix single-quoted YAML unescaping: use '' doubling (YAML spec) not
backslash escaping which only applies to double-quoted strings (greptile P1)
- Remove extraneous f-string prefix on static string (coderabbit)
- Add /prune to README command catalog and file tree (cubic)
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* fix: replace bash TOML surgery with Node add-only MCP merge
The old sync script used awk/sed to remove and re-append MCP server
sections in config.toml, causing credential extraction races, duplicate
TOML tables, and 3 fragile code paths with 9 remove_section_inplace
calls each.
Replace with a Node script (scripts/codex/merge-mcp-config.js) that
uses @iarna/toml to parse the config, then appends only missing ECC
servers — preserving all existing content byte-for-byte. Warns on
config drift, supports legacy aliases (context7 → context7-mcp), and
adds --update-mcp flag for explicit refresh.
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* fix: address PR #723 review findings for Codex MCP merge
- Use package-manager abstraction (scripts/lib/package-manager.js)
instead of hardcoding pnpm — respects CLAUDE_PACKAGE_MANAGER,
lock files, and project config
- Add Yarn 1.x fallback to npx (yarn dlx unsupported in classic)
- Add missing exa server to match .codex/config.toml baseline
- Wire up findSubSections for --update-mcp nested subtable removal
(fixes Greptile P1: Object.keys only returned top-level keys)
- Fix resolvedLabel to prefer canonical entry over legacy alias
when both exist (fixes context7/context7-mcp spurious warning)
- Fix removeSectionFromText to handle inline TOML comments
- Fix dry-run + --update-mcp to show removals before early return
- Update README parity table: 4 → 7 servers, TOML-parser-based
- Add non-npm install variants to README Codex quick start
- Update package-lock.json for @iarna/toml
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* fix: address PR #723 review comments (preflight, marker validation)
- Add Node.js and merge-mcp-config.js to preflight checks so the
script fails fast before partial writes (CodeRabbit)
- Validate marker counts: require exactly 1 BEGIN + 1 END in correct
order for clean replacement (CodeRabbit)
- Corrupted markers: strip all marker lines and re-append fresh block,
preserving user content outside markers instead of overwriting
- Move MCP_MERGE_SCRIPT to preflight section, remove duplicate
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* fix(install): add rust, cpp, csharp to legacy language alias map
The legacy installer compatibility layer in install-manifests.js was
missing entries for rust, cpp, and csharp — languages that have
rules/ directories and (for rust/cpp) install-components.json entries.
Running `./install.sh rust` fails with "Unknown legacy language: rust"
because LEGACY_LANGUAGE_ALIAS_TO_CANONICAL and
LEGACY_LANGUAGE_EXTRA_MODULE_IDS didn't include these languages.
Fixes the issue reported in #694 by @mpiton.
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* fix(install): complete csharp legacy support and add resolution tests
- Add lang:csharp component to install-components.json with
framework-language module (matching cpp/rust pattern)
- Update csharp mapping in LEGACY_LANGUAGE_EXTRA_MODULE_IDS from
empty array to ['framework-language']
- Add end-to-end resolution tests for rust, cpp, and csharp verifying
framework-language module is included in resolved moduleIds
Addresses review feedback from Copilot, Greptile, CodeRabbit, and Cubic.
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The sync script previously overwrote ~/.codex/AGENTS.md on every run,
destroying any user-authored content. This adds marker-based merging
(<!-- BEGIN ECC --> / <!-- END ECC -->) so only the ECC-managed section
is replaced on subsequent runs, preserving user content outside the
markers.
Merge logic:
- No file → create with markers
- Both markers present (ordered, CRLF-safe) → replace only the ECC section
- BEGIN without END (corrupted) → full replace (backup saved)
- No markers at all → append ECC block (preserves existing content)
Also fixes:
- Symlink preservation: uses cat > instead of mv to write through symlinks
- CRLF handling: strips \r in marker detection to handle Windows-edited files
- Marker ordering: validates BEGIN appears before END, not just that both exist
The legacy heading-match heuristic was intentionally removed per council
review: any unmarked file is either user-authored (append is safe) or
legacy ECC-generated (duplicates once, deduplicates on next run via
markers). A timestamped backup is always saved before any mutation.
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* fix(tests): skip bash tests on Windows and fix USERPROFILE in resolve-ecc-root
- hooks.test.js: add SKIP_BASH guard for 8 bash-dependent tests
(detect-project.sh, observe.sh) while keeping 207 Node.js tests running
- resolve-ecc-root.test.js: add USERPROFILE to env overrides in 2
INLINE_RESOLVE tests so os.homedir() resolves correctly on Windows
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* fix(tests): handle BOM in shebang stripping and skip worktree tests on Windows
- validators.test.js: replace regex stripShebang with character-code
approach that handles UTF-8 BOM before shebang line
- detect-project-worktree.test.js: skip entire file on Windows since
tests invoke bash scripts directly
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