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refactor: restructure skills directory and add thinking-and-docs skills

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skills/engineering/README.md
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# Engineering Skills
Daily code work.
## User-invoked
- [commit-staged](commit-staged/SKILL.md) — Commit staged files with a conventional commit message.
- [implement-isolation](implement-isolation/SKILL.md) — Implement a piece of work based on a spec or set of tickets in isolation.
- [implement-isolation-tmux](implement-isolation-tmux/SKILL.md) — Dispatch a child agent in an isolated git worktree to implement a piece of work based on a PRD or set of issues.
- [project-context-pack](project-context-pack/SKILL.md) — Build a bounded repo context pack (project map, codebase index, cached memory file) so later work uses fd/rg/tree-sitter/LSP instead of repeated browsing.
- [setup-skills](setup-skills/SKILL.md) — Configure this repo for the engineering skills, set up its issue tracker, triage label vocabulary, and domain doc layout. Run once before first use of the other engineering skills.
## Model-invoked
- [lsp-code-analysis](lsp-code-analysis/SKILL.md) — Semantic code analysis via LSP. Navigate code (definitions, references, implementations), search symbols, preview refactorings, and get file outlines. Use for exploring unfamiliar codebases or performing safe refactoring.