Preserve the original contributor histories and apply the exact independently reviewed repair.
Source-Parent: 81df6475b2
Review-Manifest-SHA256: 272ae1970f0b94fe40dbb974b509b7333682176259f5a1493bbae12d9a7e70cb
The project-scoped reference file shipped an active [profiles.yolo] block
with approval_policy = "never" and exposed MCP servers / approval_policy /
sandbox_mode / notify / profiles.* keys that override the user's own
~/.codex/config.toml when the repo is trusted. AgentShield flags this as
codex-approval-never (CRITICAL) and codex-project-config-escalates (HIGH).
Restrict the project-scoped file to model selection, persistent
instructions, features, and role definitions. Move every other key into a
clearly-marked USER-LEVEL REFERENCE appendix as commented-out examples so
installs still ship a usable template without overriding user policy.
Verified locally with ecc-agentshield scan --path . against .codex/config.toml:
* pre-fix: 2 critical/high findings
* post-fix: 0 critical/high findings
Refs: ARU-10 (ECC-SEC-1.1 review CLEAR), ARU-18 (this PR).
Co-Authored-By: Paperclip <noreply@paperclip.ing>
The global sanity check (check-codex-global-state.sh) hard-fails when
persistent_instructions is missing from ~/.codex/config.toml, but neither
the baseline .codex/config.toml nor the sync script ever define this field.
This causes a clean install to report a failing sanity check even though the
sync otherwise succeeds (#967).
- Add persistent_instructions to the baseline .codex/config.toml so that
users who cp the config get a working default.
- Downgrade the sanity check from fail to warn, since persistent_instructions
is additive and optional — users who rely solely on AGENTS.md should not be
blocked.
Fixes#967 (persistent_instructions part; context7 naming addressed by #970)
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Signed-off-by: Lidang-Jiang <lidangjiang@gmail.com>
On first startup, npx-based MCP servers need to download packages before
they can respond. The default timeout is too short for this, causing
frequent "timed out after 10 seconds" errors reported in #544.
Add startup_timeout_sec = 30 to all five command-based MCP servers
(github, context7, memory, playwright, sequential-thinking). The URL-based
exa server is unaffected and left unchanged.
30 seconds was chosen over the 20s precedent in merge-mcp-config.js to
give extra headroom for slow networks on first run.
Fixes#544
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Signed-off-by: Lidang-Jiang <lidangjiang@gmail.com>
* 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.
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>
* 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
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>
* 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>
haelyra