[BUG] Cowork only loads 3/27 personal skills from ~/.claude/skills/ — UI does not scan directory

Summary

Cowork only loads 3 out of 27 personal skills from ~/.claude/skills/, despite all 27 having valid YAML frontmatter (name: and description: fields), valid SKILL.md files, correct directory structure, and proper file permissions. 20+ hours of engineering time spent trying to fix this, and all Cowork/chat session history permanently lost after a destructive troubleshooting step that resolved nothing.

Environment

• Platform: macOS, Mac Mini M-series
• App: Claude Desktop (Cowork mode)
• Plan: Claude Max

The Paradox

Inside a Cowork session, Claude CAN see and use all 27 skills — they appear in the session's available_skills list and can be invoked with the Skill tool. The skill content works perfectly.

In the Customize → Skills panel, only 3 personal skills appear: canvas-design, skill-creator, theme-factory. The other 24 are invisible.

This means the underlying skill-loading mechanism works, but the UI management layer does not scan the same directory, creating an inconsistency where skills work but cannot be managed.

Key Observation

The 3 skills that DO load were originally installed through the Cowork Customize UI. The 24 that do NOT load were deployed to ~/.claude/skills/ via rsync/file copy from a GitHub repo. This strongly suggests Cowork maintains an internal registry of "known" skills and does NOT scan ~/.claude/skills/ at startup to discover new skill folders — contrary to documentation.

Steps to Reproduce

1. Place 27 skill folders in ~/.claude/skills/, each containing a SKILL.md with valid YAML frontmatter (---, name:, description:)
2. Verify all pass frontmatter validation and total description budget is under 16K characters
3. Quit Claude desktop app (Cmd+Q) and reopen
4. Open Cowork → Customize → Skills
5. Result: Only 3 personal skills appear. The other 24 are not listed.

What We Tried (All Failed)

1. ✅ Fixed YAML frontmatter on all skills (10 were missing name: or description: — all fixed)
2. ✅ Trimmed descriptions to fit 16K SLASH_COMMAND_TOOL_CHAR_BUDGET — currently at 7,294/16,000 chars (45%)
3. ✅ Removed all skills from Customize and restarted — only same 3 reappear
4. ✅ Ran deploy.sh --force with rsync — confirmed 27 skills deployed with valid frontmatter
5. ✅ Restarted Claude desktop app multiple times
6. ✅ Built automated deployment pipeline with frontmatter validation, budget monitoring, webhook alerts
7. ❌ Deleted ~/Library/Application Support/Claude/local-agent-mode-sessions/ to clear cached data — lost ALL Cowork and chat session history permanently. Skills still did not load. Data is unrecoverable (no Time Machine backup).

Deploy Script Output (Confirming Everything Works at File Level)

[2026-04-19 10:40:02] Excluding 25 skills from Cowork (see .cowork-exclude)
[2026-04-19 10:40:02] ✓ All 52 skills have valid frontmatter
[2026-04-19 10:40:02] 📊 Budget: 7294/16000 chars (45%) across 27 Cowork skills
[2026-04-19 10:40:02] ✓ Budget healthy (45%)
[2026-04-19 10:40:02] ✓ Claude skills updated (27 deployed)

Technical Details

• Skills directory: ~/.claude/skills/ (rwxr-xr-x permissions)
• Skills on disk: 27 folders, each with SKILL.md containing valid YAML frontmatter
• Skills that load (3): canvas-design, skill-creator, theme-factory
• Skills that do NOT load (24): agentic-development, airtable-ops, automation-pipeline-ops, cfo-advisor, champion-proof-proposal, cold-outreach, consolidate-memory, contract-and-proposal-writer, docx, intent-engineering, karpathy-loop-seo, lead-magnets, offer-stack-builder, pdf, pptx, sales-enablement, strategic-presentation-creator, superpowers, tii-executive-coach, vibe-coding, xlsx, tii-brand-voice-guardian, tii-content-repurposing, schedule
• Source: GitHub repo with automated deploy pipeline (scripts/deploy.sh)

Business Impact

• 20+ hours of engineering time across 12 days (April 7–19, 2026) building deployment infrastructure that works perfectly at the file system level but is ignored by Cowork's skill detection
• All Cowork session history and chat history permanently destroyed while attempting to troubleshoot this bug — on the suggestion that clearing session data might fix skill detection (it didn't, and the two systems are unrelated)
• We are a coaching institute (The Integral Institute) with 79 custom skills powering daily operations — executive coaching, SEO content pipeline (235+ articles), client proposals, cold outreach. Without reliable skill loading, our AI workflow is broken.

Requested Fix

1. Cowork must scan ~/.claude/skills/ on startup and detect ALL valid skills with YAML frontmatter, not only those previously registered through the UI
2. Add a "Rescan" button in Customize → Skills to manually trigger skill discovery from disk
3. Or provide a CLI command (e.g., claude skills scan) to register skills from disk
4. Document the exact mechanism for personal skill auto-detection — what triggers registration, what the hidden registry is, how power users can manage it
5. Never suggest deleting session data (local-agent-mode-sessions/) as a troubleshooting step for skill detection issues — the two systems are unrelated

Related Issues

• #28068 — Cowork fails to uninstall locally-uploaded plugins
• #28554 — Cannot uninstall plugin: enabledPlugins false ignored, plugin re-installs every session