fix(skills): remove empty plugins on skill removal

[christso]

Summary

• remove the whole plugin entry when removing a skill would leave that plugin with zero enabled skills
• keep multi-skill plugins installed and remove only the selected skill when other skills remain enabled
• share the removal logic between the CLI command and TUI, and cover the edge cases with unit tests

E2E

Single-skill GitHub source

cd /tmp/allagents-remove-skill-red-9vBqlQ/demo
HOME=/tmp/allagents-remove-skill-red-9vBqlQ/home node /home/entity/projects/EntityProcess/allagents.worktrees/fix-remove-skill-cleanup/dist/index.js skill remove llm-wiki
HOME=/tmp/allagents-remove-skill-red-9vBqlQ/home node /home/entity/projects/EntityProcess/allagents.worktrees/fix-remove-skill-cleanup/dist/index.js update

Verified:

• skill remove llm-wiki prints Removed plugin
• .allagents/workspace.yaml ends with plugins: []
• update reports Updating 0 plugin(s)
• no skill remains under the synced skill directories

Multi-skill local plugin

cd /tmp/allagents-remove-skill-red-9vBqlQ/multi
node /home/entity/projects/EntityProcess/allagents.worktrees/fix-remove-skill-cleanup/dist/index.js skill remove skill-a
node /home/entity/projects/EntityProcess/allagents.worktrees/fix-remove-skill-cleanup/dist/index.js update

Verified:

• skill remove skill-a removes only skill-a
• .allagents/workspace.yaml keeps the plugin with skills: [skill-b]
• update still syncs exactly one skill from that plugin

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