[BUG] Custom command in ~/.claude/commands/ not recognized

/tmp/gh-comment-41243.md

Found 3 possible duplicate issues:

1. https://github.com/anthropics/claude-code/issues/27888
2. https://github.com/anthropics/claude-code/issues/35346
3. https://github.com/anthropics/claude-code/issues/36486

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🤖 Generated with Claude Code

I can make them come back by using 2.1.87, go away again with 2.1.88.

I'm starting to experience exactly the same issue right now, specifically after upgrading to v2.1.88.

Context

• Everything was working fine before
• The issue started immediately after using version 2.1.88
• No changes were made on my side

What I’m seeing

• Same behavior described in this issue
• Happens consistently

Environment

• OS: Linux
• Claude Code version: 2.1.88

Notes

• The timing strongly suggests a regression introduced in v2.1.88 rather than a local setup issue

Same, updated to v2.1.88, no longer recognizing ~/.claude/commands folder, shows unknow skills

Not sure if this applies for others but my commands and agents weren't working as well. Started looking into rolling back the version. Then I thought about the 'claude has switched to a native installer use claude install' message I had been ignoring. Tried claude install, it did its thing and when I started a new session the commands and agents were working again. Hope this helps someone else.

I'm using Claude via the Windows 11 Desktop app. After the last update commands no longer work. I've been using things like /btw yesterday just fine. Also I have no %USERPROFILE%/.claude/commands folder but I'm honestly not sure if there ever has been one (but I guess so since I could use commands beforehand jsut fine).
Claude for Windows Version: Version 1.1.9669

Not sure if this applies for others but my commands and agents weren't working as well. Started looking into rolling back the version. Then I thought about the 'claude has switched to a native installer use claude install' message I had been ignoring. Tried claude install, it did its thing and when I started a new session the commands and agents were working again. Hope this helps someone else.

this worked for me

Thanks @jamesnagle for the fix — claude install re-linking resolves this for CLI users.
Summary for anyone landing here:
| Platform | Fix |
|---|---|
| CLI (npm/native) | Run claude install to re-register the native installer. Restart your terminal afterward. |
| Windows Desktop app | This appears to be a separate regression in v1.1.9669 (@Elia31's case). The Desktop app manages its own command discovery path. If %USERPROFILE%\.claude\commands\ doesn't exist, try creating it manually and placing your .md command files there, then restart the app. |
If claude install doesn't work:

which claude
claude --version
ls -la ~/.claude/commands/
claude /help  # Should list your custom commands

The root cause seems to be that v2.1.88's migration to the native installer changed how command paths are resolved. Running claude install re-establishes the correct symlinks.

Thanks @jamesnagle claude install fixed this for me.

Root Cause: vendored ripgrep binary missing execute permission

I debugged this extensively and found the actual root cause — it's not a path resolution issue but a file permission issue on the bundled rg binary.

How commands are loaded

Claude Code loads custom commands via its vendored ripgrep:

voz() → vh1() → LF() → spawn("rg", ["--files", "--glob", "*.md", path])

What went wrong in v2.1.88

The vendored ripgrep binary was installed with 644 (no execute bit):

$ ls -la /opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/vendor/ripgrep/arm64-darwin/rg
-rw-r--r--  ...  rg    # ← missing execute permission

When rg can't execute, the spawn fails with EACCES. The error handler in e44() catches this and returns an empty array []. The outer try/catch in voz() silently swallows the error — so custom commands simply vanish with no error message.

Skills (loaded via Node.js readdir() + readFile()) are unaffected since they don't depend on ripgrep.

Fix

chmod +x /opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/vendor/ripgrep/arm64-darwin/rg

For Linux users, the path is typically:

chmod +x /usr/lib/node_modules/@anthropic-ai/claude-code/vendor/ripgrep/x64-linux/rg
# or wherever `npm root -g` points to

General command to find and fix it:

chmod +x "$(npm root -g)/@anthropic-ai/claude-code/vendor/ripgrep/"*/rg

Why claude install also works

claude install likely re-extracts or re-links the binary with correct permissions as a side effect, which is why it resolves the issue for some users.

Diagnosis

# Check if rg has execute permission:
ls -la "$(npm root -g)/@anthropic-ai/claude-code/vendor/ripgrep/"*/rg

# Test if rg can actually run:
"$(npm root -g)/@anthropic-ai/claude-code/vendor/ripgrep/"*/rg --version

# Test command scanning:
"$(npm root -g)/@anthropic-ai/claude-code/vendor/ripgrep/"*/rg --files --glob "*.md" ~/.claude/commands/

Suggestion for Anthropic

The post-install script (YK4()) handles codesign and quarantine removal but doesn't ensure the execute bit. Adding chmod +x to the install/update pipeline would prevent this regression.

Great root cause analysis @luke-timon — the 644 permission on the vendored rg binary explains everything. My earlier comment incorrectly attributed this to path resolution; the execute-bit issue is the actual culprit.
For anyone landing here:
| Root cause | Vendored rg binary shipped with 644 (no execute bit) in v2.1.88 |
|---|---|
| Why it breaks | Claude Code discovers custom commands via rg --files --glob "*.md" — if rg can't execute, no commands are found |
| CLI fix | claude install (re-registers the native installer, restores permissions) |
| Windows Desktop | Separate regression in v1.1.9669 — Desktop app manages its own command discovery path |

I debugged this extensively and found the actual root cause — it's not a path resolution issue but a file permission issue on the bundled rg binary. ### How commands are loaded Claude Code loads custom commands via its vendored ripgrep:

That did it. awesome

LOL, you guys released 2.1.89 with the same bug! Unbelievable, nice work!

@TacoTakumi The fix keeps regressing because each npm install overwrites the binary with the same 644 permissions from the package tarball.

Quick fix (run once after each update):

chmod +x "$(find "$(dirname "$(readlink -f "$(which claude)")")/../vendor/ripgrep" -name rg 2>/dev/null)"

Permanent fix — add a SessionStart hook that auto-corrects the permission on every launch. In ~/.claude/settings.json:

{
  "hooks": {
    "SessionStart": [
      {
        "matcher": "",
        "hooks": [
          {
            "type": "command",
            "command": "for rg in \"$(dirname \"$(readlink -f \"$(which claude)\")\")\"/../../vendor/ripgrep/*/rg; do [ -f \"$rg\" ] && [ ! -x \"$rg\" ] && chmod +x \"$rg\"; done"
          }
        ]
      }
    ]
  }
}

This runs in <1ms and silently no-ops when the permission is already correct. It'll survive every future update until Anthropic fixes the packaging.

This issue occurred in 2.1.88 and should be fixed as of 2.1.90.

This issue has been automatically locked since it was closed and has not had any activity for 7 days. If you're experiencing a similar issue, please file a new issue and reference this one if it's relevant.