v2: /skills shows deleted and permission-disabled skills

Summary

OpenCode V2 has two issues with the /skills catalog:

1. Skills deleted from ~/.agents/skills remain visible after restarting opencode2 and reopening the TUI. They disappear only after exiting and restarting WSL2.
2. Skills disabled through the permissions settings remain visible in the /skills catalog after closing and reopening the TUI.

There are no other skill files or skill directories in this environment. All user skills are located under ~/.agents/skills.

Environment

• opencode version: opencode2 v0.0.0-next-16953
• OS: Linux 6.6.87.2-microsoft-standard-WSL2, x86_64
• Terminal: TERM=xterm-256color; TERM_PROGRAM and COLORTERM were not set
• Shell: /bin/bash
• Install/channel: next
• Active plugins: /home/wuyao/.config/opencode/plugins/session-warming-opt-in.ts
• Configured plugins: no plugins configured in /home/wuyao/.config/opencode/opencode.json
• Skill locations: all skills are under ~/.agents/skills; no other skill files or directories are present

Reproduction

Deleted skills remain visible

1. Start opencode2 in a workspace.
2. Open /skills and verify that a skill from ~/.agents/skills is present.
3. Exit opencode2.
4. Delete one or more skill directories from ~/.agents/skills.
5. Confirm that the deleted skill directories no longer exist.
6. Start opencode2 again and open /skills.
7. Observe that the deleted skills are still listed.
8. Exit WSL2 completely and restart WSL2.
9. Start opencode2 again.
10. Observe that the deleted skills are no longer listed.

Permission-disabled skills remain visible

1. Open the permissions settings.
2. Disable one or more skills.
3. Close the TUI.
4. Reopen the TUI and open /skills.
5. Observe that the disabled skills are still listed.

Expected Behavior

• The /skills catalog should reflect the current contents of ~/.agents/skills after restarting opencode2.
• Deleted skills should no longer be listed without restarting the entire WSL2 environment.
• Skills disabled through permissions should not appear in the /skills picker, or their disabled state should be clearly represented.
• A disabled skill should not be loadable or executable when its permission is denied.

Actual Behavior

• Skills deleted from ~/.agents/skills remain visible after restarting opencode2 and reopening the TUI.
• The deleted skills disappear only after exiting and restarting WSL2.
• Skills disabled through permissions remain visible after closing and reopening the TUI.
• It has not yet been confirmed whether permission-disabled skills can still be loaded or executed; the observed issue is that they remain visible in the catalog.

Additional Context

• The exact skill names and permission configuration are omitted from this report.
• The deleted-skill issue is reproducible across an opencode2 restart.
• Restarting WSL2 clears the stale skills from the catalog.
• No logs or stack traces are currently available.
• The active plugin does not configure or provide skills.
• There are no project-local or alternative skill directories in this environment.