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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* 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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---------
Co-authored-by: Claude <noreply@anthropic.com>
Co-authored-by: Happy <yesreply@happy.engineering>
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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haelyra