docs: restructure skill catalog and standardize setup-skills references

Reorganize README.md with category sections (engineering, pkm, etc.)
for both user-invoked and model-invoked skills. Add new subcategory
READMEs for skill-authoring and thinking-and-docs. Replace
/setup-matt-pocock-skills references with setup-skills across all SKILLs.

skills/engineering/README.md

@@ -5,11 +5,27 @@ 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.
+- [grill-with-docs](grill-with-docs/SKILL.md) — Interview the user to sharpen a plan or design while creating ADRs and glossary docs.
+- [implement](implement/SKILL.md) — Implement a piece of work from a spec or set of tickets.
+- [implement-isolation](implement-isolation/SKILL.md) — Implement a piece of work from a spec or set of tickets in isolation.
+- [implement-isolation-tmux](implement-isolation-tmux/SKILL.md) — Dispatch an isolated worktree agent to implement work from a PRD or issues.
+- [improve-codebase-architecture](improve-codebase-architecture/SKILL.md) — Find and work through opportunities to deepen a codebase's architecture.
+- [project-context-pack](project-context-pack/SKILL.md) — Build a bounded project context pack for later agent work.
+- [setup-skills](../setup-skills/SKILL.md) — Configure engineering skills, issue tracking, triage labels, and domain docs.
+- [to-spec](to-spec/SKILL.md) — Turn the current conversation into a spec and publish it to the issue tracker.
+- [to-tickets](to-tickets/SKILL.md) — Break a plan or spec into tracer-bullet tickets with dependencies.
+- [triage](triage/SKILL.md) — Triage issues and external PRs through the project workflow.
+- [wayfinder](wayfinder/SKILL.md) — Plan large work as decision tickets and resolve them step by step.
 
 ## 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.
+- [code-review](code-review/SKILL.md) — Review changes against repository standards and the originating specification.
+- [codebase-design](codebase-design/SKILL.md) — Design and improve deep module interfaces and seams.
+- [diagnosing-bugs](diagnosing-bugs/SKILL.md) — Diagnose hard bugs and performance regressions.
+- [domain-modeling](domain-modeling/SKILL.md) — Build and sharpen a project's domain model.
+- [lsp-code-analysis](lsp-code-analysis/SKILL.md) — Navigate code and analyze it semantically with LSP.
+- [prototype](prototype/SKILL.md) — Build a throwaway prototype to answer a design question.
+- [research](research/SKILL.md) — Investigate a question using high-trust sources and capture the findings.
+- [resolving-merge-conflicts](resolving-merge-conflicts/SKILL.md) — Resolve an in-progress Git merge or rebase conflict.
+- [tdd](tdd/SKILL.md) — Use test-driven development for features, bugs, and integration tests.
+- [wizard](wizard/SKILL.md) — Generate an interactive wizard for steps only a human can perform.