[BUG] Slash commands from other projects appear in unrelated project sessions

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Description:

When working in Project A, slash commands defined in Project B's .claude/commands/ directory appear in the available skills list, even though Project B is a completely separate repository.

Current Behavior:
Commands from other projects the user has previously worked on appear in the skills list. These commands fail if invoked (file not found), but they clutter the available commands.

Environment:

• OS: macOS
• Claude Code version: 2.1.7

Notes:

• The commands in question are project-scoped (defined in each project's .claude/commands/ directory), not global user commands in ~/.claude/
• This suggests the skill registry is incorrectly merging/caching commands across project boundaries
• Restarting Claude Code does not fix the issue
• Clearing ~/.claude/cache/ does not fix the issue
• The phantom commands appear to persist across sessions

What Should Happen?

Only commands from the current project's .claude/commands/ directory should appear in the skills list.

Error Messages/Logs

From ~/.claude/debug/{session-id}.txt:

[DEBUG] Loaded 11 unique skills (managed: 0, user: 0, project: 0, legacy commands: 11)
[DEBUG] Skills and commands included in Skill tool:
  groupA:cmd1, groupA:cmd2, groupA:cmd3, groupA:cmd4, groupA:cmd5, groupA:cmd6,
  groupB:cmd1, groupC:cmd1, groupC:cmd2,
  otherproject:cmd1, otherproject:cmd2
  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ These are from a DIFFERENT repository

Note: This project's .claude/commands/ contains 3 subdirectories (groupA/, groupB/, groupC/)
with 9 total commands. The 2 "otherproject:*" commands do NOT exist in this project -
they leak in from a completely separate repository I previously worked on.

Steps to Reproduce

1. Create Project A with custom commands in .claude/commands/projectA/command1.md
2. Create Project B with different commands in .claude/commands/projectB/command2.md
3. Open Claude Code in Project A
4. Observe that /projectB:command2 appears in the available skills list

Claude Model

Not sure / Multiple models

Is this a regression?

Yes, this worked in a previous version

Last Working Version

2.1.0

Claude Code Version

2.1.7

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Cursor

Additional Information

_No response_