Merge pull request #261 from notque/fix/reference-md-audit-unit7

fix: sync REFERENCE.md with actual codebase state

Author: notque

docs/REFERENCE.md

@@ -13,6 +13,20 @@ The primary entry point is `/do`, which routes your request to the appropriate a
 |---------|---------|---------|
 | `/do` | **Smart router** - figures out what you need | `/do debug this failing test` |
 
+### Other Slash Commands
+| Command | Purpose |
+|---------|---------|
+| `/install` | Verify toolkit installation, diagnose issues, guide setup |
+| `/pr-review` | Comprehensive PR review with retro knowledge capture |
+| `/retro` | Learning system: stats, search, audit, graduate learnings |
+| `/reddit-moderate` | Reddit moderation: modqueue, classification, actions |
+| `/generate-claudemd` | Generate project-specific CLAUDE.md from repo analysis |
+| `/github-notifications` | Triage GitHub notifications: fetch, classify, report |
+| `/create-pipeline` | Create a new pipeline from a task description |
+| `/system-upgrade` | Systematic upgrade of agents, skills, hooks |
+| `/perses-onboard` | First-time Perses setup: server, MCP, project |
+| `/github-profile-rules` | Extract coding conventions from GitHub profiles |
+
 ### Available via `/do` Routing
 These workflows are activated through `/do` with natural language:
 
@@ -77,36 +91,40 @@ Request deep expertise: *"Use the [name] agent"*
 ### Core Engineering
 | Agent | Domain |
 |-------|--------|
-| `golang-general-engineer` | Go 1.24+, concurrency, testing (with frontmatter hooks) |
-| `golang-general-engineer-compact` | Go - lightweight version for simple tasks |
-| `python-general-engineer` | Python, async, typing, pytest (with frontmatter hooks) |
-| `python-openstack-engineer` | OpenStack, Oslo libraries |
-| `typescript-frontend-engineer` | TypeScript 5+, React patterns |
-| `typescript-debugging-engineer` | TypeScript debugging, race conditions, async issues |
-| `nodejs-api-engineer` | Node.js APIs, Express, auth |
+| `golang-general-engineer` | Go 1.26+, debugging, code review, performance (with frontmatter hooks) |
+| `golang-general-engineer-compact` | Go - compact version for tight context budgets |
+| `python-general-engineer` | Python 3.12+, debugging, code review, performance (with frontmatter hooks) |
+| `python-openstack-engineer` | OpenStack: Nova, Neutron, Cinder, Oslo libraries, WSGI middleware |
+| `kotlin-general-engineer` | Kotlin: features, coroutines, debugging, code quality, multiplatform |
+| `php-general-engineer` | PHP 8.x: features, debugging, code quality, security, modern patterns |
+| `swift-general-engineer` | Swift: iOS, macOS, server-side Swift, SwiftUI, concurrency, testing |
+| `typescript-frontend-engineer` | TypeScript frontend architecture: type-safe components, state management |
+| `typescript-debugging-engineer` | TypeScript debugging: race conditions, async/await issues, type errors |
+| `nodejs-api-engineer` | Node.js backends: Express APIs, REST endpoints, middleware |
 
 ### Infrastructure & Operations
 | Agent | Domain |
 |-------|--------|
-| `kubernetes-helm-engineer` | K8s, Helm, OpenStack-on-K8s |
-| `opensearch-elasticsearch-engineer` | Search clusters, optimization |
-| `prometheus-grafana-engineer` | Monitoring, alerting, dashboards |
-| `rabbitmq-messaging-engineer` | Message queues, HA clustering |
-| `ansible-automation-engineer` | Infrastructure automation |
+| `kubernetes-helm-engineer` | Kubernetes and Helm: deployments, troubleshooting, cloud-native infrastructure |
+| `opensearch-elasticsearch-engineer` | OpenSearch/Elasticsearch: cluster management, performance tuning |
+| `prometheus-grafana-engineer` | Prometheus and Grafana: monitoring, alerting, dashboard design, PromQL |
+| `rabbitmq-messaging-engineer` | RabbitMQ: message queue architecture, clustering, HA, routing patterns |
+| `ansible-automation-engineer` | Ansible: playbooks, roles, collections, Molecule testing, Vault |
 
 ### Frontend & UI
 | Agent | Domain |
 |-------|--------|
-| `react-portfolio-engineer` | Portfolio sites, galleries |
-| `nextjs-ecommerce-engineer` | E-commerce, Stripe, auth |
-| `ui-design-engineer` | Design systems, Tailwind, a11y |
+| `react-portfolio-engineer` | React portfolio/gallery sites for creatives: React 18+, Next.js App Router |
+| `nextjs-ecommerce-engineer` | Next.js e-commerce: shopping cart, Stripe payments, checkout flows |
+| `ui-design-engineer` | UI/UX design: design systems, responsive layouts, accessibility, animations |
 
 ### Quality & Testing
 | Agent | Domain |
 |-------|--------|
-| `testing-automation-engineer` | Vitest, Playwright, E2E |
-| `performance-optimization-engineer` | Core Web Vitals, bundles |
-| `database-engineer` | PostgreSQL, Prisma, migrations |
+| `testing-automation-engineer` | Testing strategy, E2E setup, Playwright tests, test infrastructure |
+| `performance-optimization-engineer` | Web performance: Core Web Vitals, rendering, bundle analysis |
+| `database-engineer` | Database design, optimization, query performance, migrations, indexing |
+| `data-engineer` | Data pipelines, ETL/ELT, warehouse design, dimensional modeling |
 | `reviewer-code` | Code quality: conventions, naming, dead code, performance, types, tests |
 | `reviewer-system` | System review: security, concurrency, errors, observability, APIs |
 | `reviewer-domain` | Domain-specific: ADR compliance, business logic, SAP CC structural |
@@ -116,14 +134,18 @@ Request deep expertise: *"Use the [name] agent"*
 | Agent | Domain |
 |-------|--------|
 | `perses-engineer` | Perses observability platform: dashboards, plugins, operator, core |
-| `technical-documentation-engineer` | Docs, API references |
-| `technical-journalist-writer` | Technical journalism |
-| `skill-creator` | Create new skills |
-| `hook-development-engineer` | Claude Code hooks |
-| `project-coordinator-engineer` | Multi-agent orchestration |
-| `research-coordinator-engineer` | Research coordination |
-| `mcp-local-docs-engineer` | MCP server development |
-| `sqlite-peewee-engineer` | SQLite with Peewee ORM |
+| `technical-documentation-engineer` | Technical documentation: API docs, architecture, runbooks |
+| `technical-journalist-writer` | Technical journalism: explainers, opinion pieces, analysis articles |
+| `hook-development-engineer` | Python hook development for Claude Code event-driven system |
+| `project-coordinator-engineer` | Multi-agent project coordination: task breakdown, progress tracking |
+| `research-coordinator-engineer` | Research coordination: systematic investigation, multi-source analysis |
+| `research-subagent-executor` | Research subagent execution: OODA-loop investigation, source evaluation |
+| `mcp-local-docs-engineer` | MCP server development for local documentation access |
+| `sqlite-peewee-engineer` | SQLite with Peewee ORM: model definition, query optimization |
+| `pipeline-orchestrator-engineer` | Pipeline orchestration: scaffold multi-component workflows |
+| `system-upgrade-engineer` | Systematic toolkit upgrades: adapt agents, skills, hooks after updates |
+| `toolkit-governance-engineer` | Toolkit governance: edit skills, update routing tables, manage ADRs |
+| `github-profile-rules-engineer` | Extract coding conventions and style rules from GitHub user profiles |
 
 ### Voice Writers
 | Agent | Domain |
@@ -152,16 +174,16 @@ Loaded automatically or via `Skill("name")`.
 |-------|---------|
 | `workflow` | Structured multi-phase workflows (review, debug, refactor, deploy, create, research) |
 | `test-driven-development` | RED-GREEN-REFACTOR enforcement |
-| `systematic-debugging` | Reproduce → Isolate → Identify → Verify |
-| `systematic-refactoring` | CHARACTERIZE → PLAN → EXECUTE → VALIDATE |
 | `verification-before-completion` | Never done without verification |
 | `planning-with-files` | Manus-style persistent markdown planning |
 | `plan-manager` | Plan lifecycle management |
+| `git-commit-flow` | Phase-gated git commit workflow with validation |
+| `pr-workflow` | Pull request lifecycle: sync, review, fix, status, cleanup, PR mining |
 
 ### Workflows (formerly Pipelines)
 | Skill | Purpose |
 |-------|---------|
-| `workflow` | Structured multi-phase workflows: review, debug, refactor, deploy, create, research, and more. References in `skills/workflow/references/` contain the old pipeline definitions (research-to-article, explore-pipeline, pr-pipeline, doc-pipeline, etc.). |
+| `workflow` | Structured multi-phase workflows: review, debug, refactor, deploy, create, research, and more. References in `skills/workflow/references/` contain workflow definitions including systematic-debugging, systematic-refactoring, research-to-article, explore-pipeline, pr-pipeline, doc-pipeline, etc. |
 | `research-pipeline` | Formal 5-phase research pipeline with artifact saving and source quality gates |
 
 ### Code Quality
@@ -186,7 +208,6 @@ Loaded automatically or via `Skill("name")`.
 |-------|---------|
 | `codebase-analyzer` | Extract patterns statistically |
 | `codebase-overview` | Rapid context building |
-| `pr-workflow` | PR mining is part of the pr-workflow skill (via references) |
 
 ### Domain-Specific
 | Skill | Purpose |
@@ -245,7 +266,8 @@ What do you need?
 agents/            ← Specialized agents (one .md per agent, optional references/)
 skills/            ← Skills (one directory per skill, each with SKILL.md and optional references/)
   └─ workflow/     ← Structured multi-phase workflows (formerly pipelines/)
-      └─ references/  ← Old pipeline definitions loaded on demand
+      └─ references/  ← Workflow definitions loaded on demand
+commands/          ← Slash commands (one .md per command)
 hooks/             ← Python hooks and utility scripts
   └─ lib/          ← Shared libraries
 scripts/           ← Deterministic Python scripts