[Bug] Skills not detected despite files existing and permissions set

Bug Description

Output after trying to debug with CC

● According to the Skill tool, no skills are currently available - the "Available skills:" list is empty.

However, your .claude/skills/ folder contains these skill files that should be loaded:
┌────────────┬─────────┬───────────────────────────────┐
│ File │ Name │ Description │
├────────────┼─────────┼───────────────────────────────┤
│ commit.md │ commit │ Commit current changes to git │
├────────────┼─────────┼───────────────────────────────┤
│ build.md │ build │ Build the project │
├────────────┼─────────┼───────────────────────────────┤
│ run.md │ run │ Run the game │
├────────────┼─────────┼───────────────────────────────┤
│ shaders.md │ shaders │ Compile shaders │
└────────────┴─────────┴───────────────────────────────┘
And your settings.json has permissions for all of them:
"Skill(build)",
"Skill(run)",
"Skill(shaders)",
"Skill(commit)"

So there's a disconnect - the files exist, permissions are set, but Claude Code isn't detecting them. This appears to be a bug. Try restarting Claude Code to see if that helps.

Try restarting Claude Code to see if that helps.

HINT: it didn't

Environment Info

• Platform: win32
• Terminal: pycharm
• Version: 2.1.1
• Feedback ID: 682ce971-a21f-4d88-b6d4-703abe79bb41

Errors

[{"error":"Error: EPERM: operation not permitted, symlink 'C:\\Users\\User\\.claude\\projects\\C--Users-User-Workspaces-private-fna-game\\agent-ae1675e.jsonl' -> 'C:\\Users\\User\\AppData\\Local\\Temp\\claude\\C--Users-User-Workspaces-private-fna-game\\tasks\\ae1675e.output'\n    at symlinkSync (node:fs:1890:11)\n    at rWA (file:///C:/Users/User/AppData/Local/nvm/v22.15.0/node_modules/@anthropic-ai/claude-code/cli.js:1673:9724)\n    at h22 (file:///C:/Users/User/AppData/Local/nvm/v22.15.0/node_modules/@anthropic-ai/claude-code/cli.js:1830:1191)\n    at file:///C:/Users/User/AppData/Local/nvm/v22.15.0/node_modules/@anthropic-ai/claude-code/cli.js:3247:21577\n    at AsyncLocalStorage.run (node:internal/async_local_storage/async_hooks:91:14)\n    at BtA (file:///C:/Users/User/AppData/Local/nvm/v22.15.0/node_modules/@anthropic-ai/claude-code/cli.js:237:14274)\n    at Object.call (file:///C:/Users/User/AppData/Local/nvm/v22.15.0/node_modules/@anthropic-ai/claude-code/cli.js:3247:21300)\n    at process.processTicksAndRejections (node:internal/process/task_queues:105:5)","timestamp":"2026-01-08T11:21:12.268Z"},{"error":"Error: EPERM: operation not permitted, symlink 'C:\\Users\\User\\.claude\\projects\\C--Users-User-Workspaces-private-fna-game\\agent-a904c9a.jsonl' -> 'C:\\Users\\User\\AppData\\Local\\Temp\\claude\\C--Users-User-Workspaces-private-fna-game\\tasks\\a904c9a.output'\n    at symlinkSync (node:fs:1890:11)\n    at rWA (file:///C:/Users/User/AppData/Local/nvm/v22.15.0/node_modules/@anthropic-ai/claude-code/cli.js:1673:9724)\n    at h22 (file:///C:/Users/User/AppData/Local/nvm/v22.15.0/node_modules/@anthropic-ai/claude-code/cli.js:1830:1191)\n    at file:///C:/Users/User/AppData/Local/nvm/v22.15.0/node_modules/@anthropic-ai/claude-code/cli.js:3247:21577\n    at AsyncLocalStorage.run (node:internal/async_local_storage/async_hooks:91:14)\n    at BtA (file:///C:/Users/User/AppData/Local/nvm/v22.15.0/node_modules/@anthropic-ai/claude-code/cli.js:237:14274)\n    at Object.call (file:///C:/Users/User/AppData/Local/nvm/v22.15.0/node_modules/@anthropic-ai/claude-code/cli.js:3247:21300)\n    at process.processTicksAndRejections (node:internal/process/task_queues:105:5)","timestamp":"2026-01-08T11:21:12.279Z"},{"error":"Error: EPERM: operation not permitted, symlink 'C:\\Users\\User\\.claude\\projects\\C--Users-User-Workspaces-private-fna-game\\agent-af3148c.jsonl' -> 'C:\\Users\\User\\AppData\\Local\\Temp\\claude\\C--Users-User-Workspaces-private-fna-game\\tasks\\af3148c.output'\n    at symlinkSync (node:fs:1890:11)\n    at rWA (file:///C:/Users/User/AppData/Local/nvm/v22.15.0/node_modules/@anthropic-ai/claude-code/cli.js:1673:9724)\n    at h22 (file:///C:/Users/User/AppData/Local/nvm/v22.15.0/node_modules/@anthropic-ai/claude-code/cli.js:1830:1191)\n    at file:///C:/Users/User/AppData/Local/nvm/v22.15.0/node_modules/@anthropic-ai/claude-code/cli.js:3247:21577\n    at AsyncLocalStorage.run (node:internal/async_local_storage/async_hooks:91:14)\n    at BtA (file:///C:/Users/User/AppData/Local/nvm/v22.15.0/node_modules/@anthropic-ai/claude-code/cli.js:237:14274)\n    at Object.call (file:///C:/Users/User/AppData/Local/nvm/v22.15.0/node_modules/@anthropic-ai/claude-code/cli.js:3247:21300)\n    at process.processTicksAndRejections (node:internal/process/task_queues:105:5)","timestamp":"2026-01-08T11:21:12.287Z"},{"error":"Error: LSP server plugin:rust-analyzer-lsp:rust-analyzer crashed with exit code 1\n   

Note: Error logs were truncated.