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.

README.md

@@ -1,23 +1,102 @@
 # Skills
 
-Agent skills (slash commands and behaviors) loaded into my agent.
+Agent skills (slash commands and behaviors) loaded into AI coding agents.
+
+Skills are grouped by invocation type. [User-invoked](docs/invocation.md) skills run only when a person invokes them; model-invoked skills can also be selected automatically.
 
 ## User-invoked
 
-- [agent-handoff](common/in-progress/agent-handoff/SKILL.md) — Hand the current conversation off to a fresh background agent that picks up the work immediately.
-- [commit-staged](common/engineering/commit-staged/SKILL.md) — Commit staged files with a conventional commit message.
-- [conversation-summary](common/pkm/conversation-summary/SKILL.md) — Save the current conversation as a comprehensive report note in your Obsidian vault, following OKF v0.1 conventions.
-- [crit](common/pkm/crit/SKILL.md) — Run the CRIT framework — give the AI Context, assign it a Role, let it Interview you one question at a time, then issue the Task.
-- [implement-isolation](common/engineering/implement-isolation/SKILL.md) — Implement a piece of work based on a spec or set of tickets in isolation.
-- [implement-isolation-tmux](common/engineering/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.
-- [knowledge-gardener](common/in-progress/knowledge-gardener/SKILL.md) — Run vault-aware semantic search, synthesis, note creation, linking, and Zettelkasten workflows for this Obsidian vault.
-- [project-context-pack](common/engineering/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.
-- [research-vault](common/pkm/research-vault/SKILL.md) — Research a topic through a one-question-at-a-time learning conversation, answer directly, share resources when useful, and save a linked OKF-conformant research packet in the Obsidian vault.
-- [setup-skills](common/engineering/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.
-- [tmux-launch-agent](common/misc/tmux-launch-agent/SKILL.md) — Fork a new agent CLI session into a new tmux window, detected from the current agent.
-- [youtube-video-capture](common/pkm/youtube-video-capture/SKILL.md) — Fetch subtitles from a YouTube video, summarize the content, and save both the summary and raw subtitles to the Video bundle in the Obsidian vault.
+### Engineering
+
+- [commit-staged](skills/engineering/commit-staged/SKILL.md) — Commit staged files with a conventional commit message.
+- [grill-with-docs](skills/engineering/grill-with-docs/SKILL.md) — Interview the user to sharpen a plan or design while creating ADRs and glossary docs.
+- [implement](skills/engineering/implement/SKILL.md) — Implement a piece of work from a spec or set of tickets.
+- [implement-isolation](skills/engineering/implement-isolation/SKILL.md) — Implement a piece of work from a spec or set of tickets in isolation.
+- [implement-isolation-tmux](skills/engineering/implement-isolation-tmux/SKILL.md) — Dispatch an isolated worktree agent to implement work from a PRD or issues.
+- [improve-codebase-architecture](skills/engineering/improve-codebase-architecture/SKILL.md) — Find and work through opportunities to deepen a codebase's architecture.
+- [project-context-pack](skills/engineering/project-context-pack/SKILL.md) — Build a bounded project context pack for later agent work.
+- [setup-skills](skills/setup-skills/SKILL.md) — Configure engineering skills, issue tracking, triage labels, and domain docs.
+- [to-spec](skills/engineering/to-spec/SKILL.md) — Turn the current conversation into a spec and publish it to the issue tracker.
+- [to-tickets](skills/engineering/to-tickets/SKILL.md) — Break a plan or spec into tracer-bullet tickets with dependencies.
+- [triage](skills/engineering/triage/SKILL.md) — Triage issues and external PRs through the project workflow.
+- [wayfinder](skills/engineering/wayfinder/SKILL.md) — Plan large work as decision tickets and resolve them step by step.
+
+### In-progress
+
+- [agent-handoff](skills/in-progress/agent-handoff/SKILL.md) — Hand the current conversation to a fresh background agent.
+- [knowledge-gardener](skills/in-progress/knowledge-gardener/SKILL.md) — Run vault-aware search, synthesis, note creation, and linking workflows.
+
+### Miscellaneous
+
+- [bro](skills/misc/bro/SKILL.md) — Restate the last message in plain human language.
+- [tmux-launch-agent](skills/misc/tmux-launch-agent/SKILL.md) — Fork a new agent CLI session into a new tmux window.
+
+### PKM
+
+- [conversation-summary](skills/pkm/conversation-summary/SKILL.md) — Save the current conversation as a report note in an Obsidian vault.
+- [crit](skills/pkm/crit/SKILL.md) — Run the CRIT framework through context, role, interview, and task.
+- [research-vault](skills/pkm/research-vault/SKILL.md) — Research a topic through a guided conversation and save a linked vault packet.
+- [youtube-video-capture](skills/pkm/youtube-video-capture/SKILL.md) — Capture a YouTube video's subtitles and summary in an Obsidian vault.
+
+### Productivity
+
+- [grill-me](skills/productivity/grill-me/SKILL.md) — Interview the user to sharpen a plan or design.
+- [handoff](skills/productivity/handoff/SKILL.md) — Compact the current conversation into a handoff document.
+- [teach](skills/productivity/teach/SKILL.md) — Teach the user a new skill or concept within the workspace.
+- [to-questionnaire](skills/productivity/to-questionnaire/SKILL.md) — Turn an unresolved decision into a questionnaire.
+- [wait-what](skills/productivity/wait-what/SKILL.md) — Re-pitch the last message in clearer terms.
+
+### Skill authoring
+
+No user-invoked skills.
+
+### Thinking and docs
+
+- [before-building](skills/thinking-and-docs/before-building/SKILL.md) — Surface consequential choices when the user proposes a build.
+- [decisions](skills/thinking-and-docs/decisions/SKILL.md) — List choices made during the current work that remain uncertain.
+- [level-up](skills/thinking-and-docs/level-up/SKILL.md) — Assess technical and product knowledge and grow a learning plan.
+- [read-all-adrs](skills/thinking-and-docs/read-all-adrs/SKILL.md) — Read every ADR in the project's `docs/adr/` folder.
+- [remind](skills/thinking-and-docs/remind/SKILL.md) — Rewrite the last response more simply and briefly.
+- [short](skills/thinking-and-docs/short/SKILL.md) — Compress the current answer while keeping its substance.
+- [teach](skills/thinking-and-docs/teach/SKILL.md) — Teach the user a new skill or concept within the workspace.
 
 ## Model-invoked
 
-- [lsp-code-analysis](common/engineering/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.
-- [pkm-curation](common/pkm/pkm-curation/SKILL.md) — Curate an Obsidian vault — classify notes, normalize frontmatter, add links, extract atomic notes. Use when curating, batch-processing, reviewing, or doing a serendipity pick.
+### Engineering
+
+- [code-review](skills/engineering/code-review/SKILL.md) — Review changes against repository standards and the originating specification.
+- [codebase-design](skills/engineering/codebase-design/SKILL.md) — Design and improve deep module interfaces and seams.
+- [diagnosing-bugs](skills/engineering/diagnosing-bugs/SKILL.md) — Diagnose hard bugs and performance regressions.
+- [domain-modeling](skills/engineering/domain-modeling/SKILL.md) — Build and sharpen a project's domain model.
+- [lsp-code-analysis](skills/engineering/lsp-code-analysis/SKILL.md) — Navigate code and analyze it semantically with LSP.
+- [prototype](skills/engineering/prototype/SKILL.md) — Build a throwaway prototype to answer a design question.
+- [research](skills/engineering/research/SKILL.md) — Investigate a question using high-trust sources and capture the findings.
+- [resolving-merge-conflicts](skills/engineering/resolving-merge-conflicts/SKILL.md) — Resolve an in-progress Git merge or rebase conflict.
+- [tdd](skills/engineering/tdd/SKILL.md) — Use test-driven development for features, bugs, and integration tests.
+- [wizard](skills/engineering/wizard/SKILL.md) — Generate an interactive wizard for steps only a human can perform.
+
+### Miscellaneous
+
+- [migrate-to-shoehorn](skills/misc/migrate-to-shoehorn/SKILL.md) — Migrate test assertions from `as` to `@total-typescript/shoehorn`.
+- [scaffold-exercises](skills/misc/scaffold-exercises/SKILL.md) — Create linted exercise directories with problems, solutions, and explainers.
+- [setup-pre-commit](skills/misc/setup-pre-commit/SKILL.md) — Set up Husky, lint-staged, type checking, and tests.
+
+### PKM
+
+- [pkm-curation](skills/pkm/pkm-curation/SKILL.md) — Curate an Obsidian vault with classification, links, and atomic notes.
+
+### Productivity
+
+- [grilling](skills/productivity/grilling/SKILL.md) — Grill the user relentlessly about a plan or design.
+- [writing-for-agents](skills/productivity/writing-for-agents/SKILL.md) — Write effective documents for agents.
+
+### Skill authoring
+
+- [effective-agent-skills](skills/skill-authoring/effective-agent-skills/SKILL.md) — Write, review, and debug effective agent skills.
+
+### Thinking and docs
+
+- [brain-to-docs](skills/thinking-and-docs/brain-to-docs/SKILL.md) — Extract project vision, decisions, and preferences into documentation.
+- [next-decision](skills/thinking-and-docs/next-decision/SKILL.md) — Drill into the next unresolved decision with choices and a recommendation.
+- [prompt-me](skills/thinking-and-docs/prompt-me/SKILL.md) — Ask pointed questions to extract project priorities and concerns.
+- [save-idea](skills/thinking-and-docs/save-idea/SKILL.md) — Capture content ideas in the user's content backlog.