Skiller plugin conflict skip

Goal

Patch ../skiller so plugin-managed skills that conflict with local/manual skills can be skipped instead of being installed under duplicate names like compound-engineering-*.

Context

• plate has local skills in .agents/skills that already occupy names like ce-plan and document-review.
• The globally enabled compound-engineering plugin currently syncs the same items into .agents/skills under namespaced directories.
• Existing skiller behavior hardcodes conflict resolution to namespace-on-conflict.

Plan

1. Add a skills config option in skiller for plugin conflict handling.
2. Cover config parsing and plugin sync behavior with tests.
3. Pass the config through the apply path into plugin sync.
4. Set plate/.claude/skiller.toml to skip conflicting plugin items.
5. Verify skiller apply no longer regenerates the duplicate compound-engineering-* skills.

Findings

• Existing repo learnings only cover canonical agent ids in skiller.toml, not duplicate plugin skills.
• The critical-patterns file referenced by learnings-researcher does not exist in this repo.
• cloneLoadedConfig in ../skiller/src/core/apply-engine.ts currently drops skills config, so any new skills option must be threaded there too.

Verification

• ../skiller: targeted Jest tests for config parsing and plugin sync
• ../skiller: pnpm build
• ../skiller: pnpm lint:fix
• plate: bun x /Users/zbeyens/git/skiller/dist/cli/index.js apply
• plate: pnpm lint:fix