feat(deep-wiki): deploy command, mermaid zoom, focus mode, cross-references, and bug fixes

.github/plugins/deep-wiki/README.md

@@ -33,6 +33,7 @@ copilot --plugin-dir ./deep-wiki
 | `/deep-wiki:llms` | Generate `llms.txt` and `llms-full.txt` for LLM-friendly project access |
 | `/deep-wiki:ado` | Generate a Node.js script to convert wiki to Azure DevOps Wiki-compatible format |
 | `/deep-wiki:build` | Package generated wiki as a VitePress site with dark theme |
+| `/deep-wiki:deploy` | Generate GitHub Actions workflow to deploy wiki to GitHub Pages |
 
 ## Agents
 
@@ -88,6 +89,9 @@ View available agents: `/agents`
 
 # Generate llms.txt for LLM-friendly access
 /deep-wiki:llms
+
+# Deploy wiki to GitHub Pages (optional)
+/deep-wiki:deploy
 ```
 
 ## How It Works
@@ -104,6 +108,8 @@ Repository → Scan → Catalogue (JSON TOC) → Per-Section Pages → Assembled
                                          AGENTS.md Files (Only If Missing)
                                                     ↓
                                          llms.txt + llms-full.txt (LLM-friendly)
+                                                    ↓
+                                         GitHub Pages Deployment (Optional)
 ```
 
 | Step | Component | What It Does |
@@ -169,6 +175,7 @@ deep-wiki/
 │   ├── onboard.md           # Onboarding guide generation
 │   ├── agents.md            # AGENTS.md generation (only if missing)
 │   ├── llms.md              # llms.txt generation for LLM-friendly access
+│   ├── deploy.md            # GitHub Pages deployment workflow generation
 │   ├── ado.md               # Azure DevOps Wiki export script generation
 │   └── build.md             # VitePress site packaging
 ├── skills/                   # Auto-invoked based on context

.github/plugins/deep-wiki/agents/wiki-writer.md

@@ -53,6 +53,7 @@ When generating a documentation page, you ALWAYS follow this sequence:
 - **Minimum 3–5 Mermaid diagrams per page** (scaled by scope), each followed by a `<!-- Sources: ... -->` comment block
 - **Diagram variety**: Each page MUST use at least 2 different diagram types — don't just repeat `graph TB`. Mix architecture graphs, sequence diagrams, class diagrams, state machines, ER diagrams, and flowcharts as appropriate
 - Minimum 5 source file citations per page using linked format (see Citation Format above)
+- **Cross-reference related wiki pages** inline using relative Markdown links (e.g., `[Data Flow](../02-architecture/data-flow.md)`) and end each page with a "Related Pages" table
 - Use `autonumber` in all sequence diagrams
 - Explain WHY, not just WHAT
 - Every section must add value — no filler content
@@ -117,4 +118,5 @@ Before finishing any page:
 - [ ] All citations use correct format (linked for remote repos, local otherwise)
 - [ ] At least 2 Mermaid diagrams present
 - [ ] At least 5 different source files cited
+- [ ] Cross-references to related wiki pages included (inline links + Related Pages section)
 - [ ] No claims without code references

.github/plugins/deep-wiki/commands/agents.md

@@ -125,6 +125,49 @@ For each folder where AGENTS.md is missing, generate a file covering the **six c
 - Should NOT repeat root-level content
 - Should be concise — the root AGENTS.md handles the big picture
 
+**Wiki AGENTS.md** (`wiki/AGENTS.md`) — Generate for the wiki folder if it doesn't already exist (same only-if-missing guard). Use this template:
+
+```markdown
+# Wiki — Agent Instructions
+
+## Overview
+Generated VitePress documentation site for this project. Contains architecture docs, onboarding guides, and API references with source-linked citations and dark-mode Mermaid diagrams.
+
+## Build & Run Commands
+- Install: `npm install`
+- Dev server: `npm run dev`
+- Build: `npm run build`
+- Preview: `npm run preview`
+
+## Wiki Structure
+- `index.md` — Landing page with project overview and navigation
+- `onboarding/` — Audience-tailored guides (contributor, staff engineer, executive, product manager)
+- `{NN}-{section}/` — Numbered documentation sections
+- `llms.txt` — LLM-friendly project summary (links + descriptions)
+- `llms-full.txt` — LLM-friendly full content (inlined pages)
+- `.vitepress/config.mts` — VitePress config with sidebar and Mermaid setup
+- `.vitepress/theme/` — Dark theme (custom.css) and zoom handlers (index.ts)
+
+## Content Conventions
+- All Mermaid diagrams use dark-mode colors (fills `#2d333b`, borders `#6d5dfc`, text `#e6edf3`)
+- Every page has VitePress frontmatter (`title`, `description`)
+- Citations link to source repository with line numbers
+- Tables include a "Source" column with linked citations
+- Mermaid diagrams followed by `<!-- Sources: ... -->` comment blocks
+
+## Boundaries
+- ✅ **Always do:** Add new pages following existing section numbering, use dark-mode Mermaid colors
+- ⚠️ **Ask first:** Change theme CSS, modify VitePress config, restructure sections
+- 🚫 **Never do:** Delete generated pages without understanding dependencies, use light-mode colors, remove citation links
+
+## Documentation
+- Wiki: `./` — This folder is the wiki
+- LLM Context: `llms.txt` — Quick summary; `llms-full.txt` — Full content
+- Onboarding: `onboarding/` — Four audience-tailored guides
+```
+
+Adapt this template to the actual project — fill in the real section names, technologies, and any project-specific conventions.
+
 ### Step 5: Generate CLAUDE.md Companion Files
 
 For every folder where you generated an `AGENTS.md`, also create a `CLAUDE.md` in the same folder — **only if `CLAUDE.md` does not already exist**.