docs: rewrite repo indexes and context pack for skills/ layout

Replace the stale common/ structure docs with the current skills/ bucket
layout. Root and bucket READMEs now index every SKILL.md by invocation
type, AGENTS.md lists the ten actual buckets, and the project context
pack is condensed to purpose, structure, conventions, and validation.

skills/engineering/README.md

@@ -4,33 +4,38 @@ Daily code work.
 
 ## User-invoked
 
+- [thermo-nuclear-code-quality-review](code-quality-review/SKILL.md) — Run an extremely strict maintainability review for abstraction quality, giant files, and spaghetti-condition growth. Use for a thermo-nuclear code quality review, thermonuclear review, deep code quality audit, or especially harsh maintainability review.
 - [commit-staged](commit-staged/SKILL.md) — Commit staged files with a conventional commit message.
-- [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.
+- [grill-with-docs](grill-with-docs/SKILL.md) — A relentless interview to sharpen a plan or design, which also creates docs (ADR's and glossary) as we go.
+- [implement](implement/SKILL.md) — Implement a piece of work based on a spec or set of tickets.
+- [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.
+- [implement-spec](implement-spec/SKILL.md) — Implement the result of /to-spec and /to-tickets in code.
+- [implementation-orchestrator](implementation-orchestrator/SKILL.md) — Implements ready-for-agent tracker tickets through isolated worktrees, pull requests, review, conflict resolution, and merge. Use after wayfinder and planning have produced tickets, with or without a ticket ID/URL; no ticket ID/URL means process available tickets. Does not create planning tickets.
+- [improve-codebase-architecture](improve-codebase-architecture/SKILL.md) — Scan a codebase for deepening opportunities, present them as a visual HTML report, then grill through whichever one you pick.
 - [orchestrate-herdr](orchestrate-herdr/SKILL.md) — Drive a plan from context or @file through a published spec, linked tickets, and one-at-a-time isolated implementation to a merged PR using Herdr and Pi agents.
-- [project-context-pack](project-context-pack/SKILL.md) — Build a bounded project context pack for later agent work.
-- [recipe-diagrams](recipe-diagrams/SKILL.md) — Convert recipes into high-resolution process-flow diagrams.
-- [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.
+- [project-context-pack](project-context-pack/SKILL.md) — Use when the user wants a bounded repo context pack, project map, codebase index, or cached memory file so later work uses fd/rg/tree-sitter/LSP instead of repeated browsing.
+- [recipe-diagrams](recipe-diagrams/SKILL.md) — Recipe diagrams: convert any recipe into a high-resolution Cooking for Engineers-style PNG process-flow table with aligned ingredient streams, preparation branches, joins, temperatures, timings, and finish steps. Use when the user asks for a recipe diagram.
+- [security-audit](security-audit/SKILL.md) — Comprehensive security and correctness audit of a branch's changes. Use for deep review requests, or branch/PR diff audits focused on bugs, breaking changes, security issues, devex regressions, and feature-gate leaks.
+- [triage](triage/SKILL.md) — Move issues and external PRs through a state machine of triage roles, categorise, verify, grill if needed, and write agent-ready briefs.
+- [wayfinder](wayfinder/SKILL.md) — Plan a huge chunk of work (more than one agent session can hold) as a shared map of decision tickets on your issue tracker, and resolve them one at a time until the way to the destination is clear.
 
 ## Model-invoked
 
-- [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.
-- [dual-review](dual-review/SKILL.md) — Run parallel correctness/security and maintainability reviews of a branch diff, then synthesize findings.
-- [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.
-- [worktrees](worktrees/SKILL.md) — Manage Git worktrees in a canonical repository root.
-- [write-discoverable-code](write-discoverable-code/SKILL.md) — Write code agents and humans can find through plain-text search.
+- [code-review](code-review/SKILL.md) — Review the changes since a fixed point (commit, branch, tag, or merge-base) along two axes: Standards (does the code follow this repo's documented coding standards?) and Spec (does the code match what the originating issue/spec asked for?). Runs both reviews in parallel sub-agents and reports them side by side. Use when the user wants to review a branch, a PR, work-in-progress changes, or asks to "review since X".
+- [codebase-design](codebase-design/SKILL.md) — Shared vocabulary for designing deep modules. Use when the user wants to design or improve a module's interface, find deepening opportunities, decide where a seam goes, make code more testable or AI-navigable, or when another skill needs the deep-module vocabulary.
+- [diagnosing-bugs](diagnosing-bugs/SKILL.md) — Diagnosis loop for hard bugs and performance regressions. Use when the user says "diagnose"/"debug this", or reports something broken/throwing/failing/slow.
+- [domain-modeling](domain-modeling/SKILL.md) — Build and sharpen a project's domain model. Use when discussing codebase terminology, writing or editing a CONTEXT.md, or recording or editing an ADR.
+- [dual-review](dual-review/SKILL.md) — Run two independent, read-only reviews of a branch diff in parallel — correctness/security and maintainability — then synthesize prioritized findings. Use for a second review axis alongside code-review, a combined deep plus code-quality audit, or when the user asks for dual review. Runs both axes as parallel sub-agents so they do not pollute each other's context.
+- [forge-cli](forge-cli/SKILL.md) — Provides copy-paste, non-interactive tea, gh, and glab commands for issue and pull or merge request work. Use whenever a task needs tracker inspection, assignment, labels, comments, reviews, CI, or merge operations.
+- [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.
+- [pr](pr/SKILL.md) — Use when writing a PR body.
+- [prototype](prototype/SKILL.md) — Build a throwaway prototype to answer a design question. Use when the user wants to sanity-check whether a state model or logic feels right, or explore what a UI should look like.
+- [research](research/SKILL.md) — Investigate a question against high-trust primary sources and capture the findings as a Markdown file in the repo. Use when the user wants a topic researched, docs or API facts gathered, or reading legwork delegated to a background agent.
+- [resolving-merge-conflicts](resolving-merge-conflicts/SKILL.md) — Use when you need to resolve an in-progress git merge/rebase conflict.
+- [tdd](tdd/SKILL.md) — Test-driven development. Use when the user wants to build features or fix bugs test-first, mentions "red-green-refactor", or wants integration tests.
+- [to-spec](to-spec/SKILL.md) — Turn the current conversation into a spec and publish it to the project issue tracker: no interview, just synthesis of what you've already discussed. Use when the user wants a spec from the current conversation or an orchestration workflow needs to publish one from context.
+- [to-tickets](to-tickets/SKILL.md) — Break a plan, spec, or the current conversation into tracer-bullet tickets with blocking edges, published to the configured tracker. Use when the user wants tickets from a plan or spec, or an orchestration workflow needs agent-grabbable tickets.
+- [wizard](wizard/SKILL.md) — Generate an interactive bash wizard that walks a human through steps only they can perform. Use when provisioning infrastructure, setting up credentials or CI secrets, walking an unfamiliar third-party dashboard, or running a one-off migration or cutover. Don't invoke this for steps the agent can perform itself.
+- [worktrees](worktrees/SKILL.md) — Manage Git worktrees in a canonical `.bare` repository root. Use when creating, reusing, listing, removing, or repairing worktrees, or when setting up a repository to keep all branch checkouts under one root.
+- [write-discoverable-code](write-discoverable-code/SKILL.md) — |