Project-root `config/` directory auto-deleted when Codex plugin installed (data loss)

Summary

When the Codex plugin (codex@openai-codex) is installed, a directory named config/ at the project root is automatically deleted by Claude Code shortly after files are written into it via the Write tool. This silently destroys user-created project structures that use config/ for application configuration.

Environment

• Claude Code: 2.1.122
• OS: macOS Darwin 25.3.0 (arm64, Apple Silicon)
• Shell: zsh
• Plugin installed: codex@openai-codex

Steps to reproduce

1. Install Codex plugin: /plugin install codex@openai-codex
2. In a project root, create a directory named config/.
3. Use the Write tool to create a text file inside it (e.g. config/settings.txt).
4. Wait a few seconds, then ls config/.

Expected behavior

The config/ directory and its contents persist.

Actual behavior

The config/ directory is deleted within seconds. ls config/ returns No such file or directory. Reproducible: each re-creation gets deleted again.

Evidence — fs_usage trace

Captured with sudo fs_usage -w -t 60 | grep "<project>/config". Process name 2.1.122.<thread_id> matches claude --version (2.1.122 (Claude Code)).

12:01:49.517046  mkdir    .../config                  mkdir.40714603       ← user mkdir
12:01:49.522554  unlinkat .../config                  2.1.122.40497423     ← deleted 5ms later
12:01:53.425295  mkdir    .../config                  2.1.122.40497475     ← Write tool re-creates
12:01:53.425525  openat   .../config/targets.txt.tmp.... 2.1.122           ← write
12:01:53.425767  rename   .../config/targets.txt      2.1.122
12:01:54.789013  openat   .../config/exclude.txt.tmp.... 2.1.122
12:01:54.789248  rename   .../config/exclude.txt      2.1.122
12:01:58.029729  unlinkat .../config                  2.1.122.40497423     ← deleted again

Eliminated causes

• PreToolUse / PostToolUse hooks examined (enforce-cwd-boundary.sh, notify-customization-change.sh) — no delete logic.
• .gitignore does not list config/.
• .claude/settings.local.json only contains permissions.
• Directories with other names under the same project (bin/, conf/) are NOT deleted.

Suspected mechanism

Codex plugin's project-root configuration discovery seems to be misclassifying user-created config/ as plugin cache and running cleanup against it. Possibly related to existing plugin-cache issues:

• #29074 — Plugin cache not cleared on uninstall/reinstall
• #37865 — Plugin uninstall leaves orphaned cache directories
• #15369 — Plugin uninstall does not clear cached files

Workaround

Use a different directory name. Confirmed working: conf/, bin/. Avoid config/ at project root while the Codex plugin is installed.

Impact

Silent data loss for user-created configuration directories. Suggested fix: scope Codex's cleanup logic strictly to plugin-managed directories.