Reproduced issue #3485 on installed Codex CLI 0.162.0. Keep user legacy choices for explicit migration and verify disposable install, repair, reinstall and removal.
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