fix: safe Codex config sync — merge AGENTS.md + add-only MCP servers (#723)

* 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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via [Happy](https://happy.engineering)

Co-Authored-By: Claude <noreply@anthropic.com>
Co-Authored-By: Happy <yesreply@happy.engineering>

* 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

Generated with [Claude Code](https://claude.ai/code)
via [Happy](https://happy.engineering)

Co-Authored-By: Claude <noreply@anthropic.com>
Co-Authored-By: Happy <yesreply@happy.engineering>

---------

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

.codex/AGENTS.md

@@ -46,6 +46,17 @@ Available skills:
 
 Treat the project-local `.codex/config.toml` as the default Codex baseline for ECC. The current ECC baseline enables GitHub, Context7, Exa, Memory, Playwright, and Sequential Thinking; add heavier extras in `~/.codex/config.toml` only when a task actually needs them.
 
+### Automatic config.toml merging
+
+The sync script (`scripts/sync-ecc-to-codex.sh`) uses a Node-based TOML parser to safely merge ECC MCP servers into `~/.codex/config.toml`:
+
+- **Add-only by default** — missing ECC servers are appended; existing servers are never modified or removed.
+- **7 managed servers** — Supabase, Playwright, Context7, Exa, GitHub, Memory, Sequential Thinking.
+- **Package-manager aware** — uses the project's configured package manager (npm/pnpm/yarn/bun) instead of hardcoding `pnpm`.
+- **Drift warnings** — if an existing server's config differs from the ECC recommendation, the script logs a warning.
+- **`--update-mcp`** — explicitly replaces all ECC-managed servers with the latest recommended config (safely removes subtables like `[mcp_servers.supabase.env]`).
+- **User config is always preserved** — custom servers, args, env vars, and credentials outside ECC-managed sections are never touched.
+
 ## Multi-Agent Support
 
 Codex now supports multi-agent workflows behind the experimental `features.multi_agent` flag.