Custom commands in .claude/commands/ not discovered after upgrading to 2.1.88

[lokkaflokka]

Description

After upgrading from Claude Code 2.1.87 to 2.1.88, custom commands defined as .md files in .claude/commands/ are no longer discovered or shown in /help → custom-commands.

Reproduction

1. Have a project with custom commands in .claude/commands/*.md (e.g., start.md, end.md, publish.md, etc.)
2. Confirm they work on 2.1.87 — all custom commands appear in /help custom-commands and are invocable
3. Upgrade to 2.1.88 (npm install -g @anthropic-ai/claude-code@latest)
4. Launch claude in the same project directory
5. Run /help → navigate to custom-commands tab

Expected

Custom commands from .claude/commands/ appear alongside bundled commands.

Actual

Only bundled commands appear (/batch, /claude-api, /debug, /loop, /schedule, /simplify, /update-config). No custom commands are shown or invocable.

Environment

• macOS (Darwin 24.6.0, Apple Silicon)
• Claude Code 2.1.88
• Model: Opus 4.6 (1M context), Claude Max
• Project has .claude/commands/ with 12+ custom .md command files
• .claude/settings.json present in project
• Parallel session on 2.1.87 in the same directory discovers all custom commands correctly

Workaround

Pin to 2.1.87: npm install -g @anthropic-ai/claude-code@2.1.87

[github-actions]

Found 3 possible duplicate issues:

1. Custom slash commands from .claude/commands/ no longer appear in autocomplete (v2.1.88) #41398
2. [BUG] slash commands not discovered in v2.1.88 #41387
3. [BUG] Custom command in ~/.claude/commands/ not recognized #41243

This issue will be automatically closed as a duplicate in 3 days.

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🤖 Generated with Claude Code

[aixohub]

Claude Code version 2.1.88 has been removed from the npm registry due to the accidental exposure of the cli.js.map file. If you visit https://www.npmjs.com/package/@anthropic-ai/claude-code/v/2.1.88, you will see a notice stating, "This version has been deprecated." However, if you still possess a copy of version 2.1.88, you can extract the source code for Claude Code directly from the cli.js.map file.

[lokkaflokka]

Update — version lock workaround:

Add "env": { "DISABLE_AUTOUPDATER": "1" } to ~/.claude/settings.json to prevent auto-update from overriding a pinned version. Then reinstall the target version (npm install -g @anthropic-ai/claude-code@2.1.87). This holds until you manually update.

Re: auto-closure as duplicate: The custom commands discovery bug in 2.1.88 matches #41398/#41387/#41243. Confirmed working on 2.1.87, broken on 2.1.88+. 2.1.88 has since been deprecated from npm (source map leak). Unclear if 2.1.89 fixes the commands issue — pinning to 2.1.87 for now.

[jdainsworthsnb]

still broken in 2.1.89

[flytomek]

still broken in 2.1.89

Fixed in 2.1.90

[marlvinvu]

My Claude says issue #41463 identified the root cause: the bundled ripgrep binary in the npm package has its execute permission stripped (644 instead of 755) → scanning .claude/commands/ fails silently → all custom commands invisible. Worth trying: find your ripgrep binary with find "$(npm root -g)/@anthropic-ai/claude-code" -name "rg" -type f then chmod +x it. If commands reappear, it's the same bug.

[ashwin-ant]

This was fixed in v2.1.91 — The bundled ripgrep binary now ships with execute permissions, restoring discovery of custom commands in .claude/commands/. If you're still seeing this in the latest version, please comment with your version and repro and we'll reopen.