feat(navigator): hero split layout, tree persistence, multi-language syntax, shallow retention, and docs overhaul

[spelech]

Summary of Changes

1. Code Navigator Fixes & Intelligence Button Responsiveness

• Immediate Intelligence Availability: Removed symbol-gating and disabled state from the Intelligence inspector tab button in NavigatorInspector.tsx. Users can immediately inspect AST intelligence upon selecting any file without having to first switch to the Symbols sidebar pane.
• Automatic AST Symbol Pre-fetching: Updated fetchOutline and tab switching in CodeNavigator.tsx to pre-select the primary symbol and fetch caller/callee impact in the background.
• Graceful Empty State: Added clear fallbacks and contextual empty states for files without AST symbol declarations.
• Copy Permalink: Restored symbol permalink copying button with unencoded file path and line number ranges.

2. Code Navigator Hero Split Layout & Tree Persistence

• Dual-Pane Sidebar: Tabbed navigation between Files (hierarchical directory tree) and Symbols (AST symbol declarations with category filter chips).
• Directory Expansion Persistence: Implemented per-repository directory expansion state persistence in NavigatorTree.tsx using sessionStorage (cc_nav_expanded_{repo}), preserving folder open/close state across tab switches and browser reloads.
• Rich Syntax Highlighting across 8+ Languages: Extended Prism tokenization with curated dark-mode color themes for C#, Python, TypeScript/JavaScript, C++, Go, Rust, SQL, and COBOL.
• Markdown Tables & Mermaid Rendering: Added automatic table normalization (bridging blank lines, synthesizing missing separator rows) and integrated Mermaid diagram rendering in NavigatorDocReader.tsx.

3. Git Repositories & Shallow Copy Retention

• Configurable Shallow Retention (keep_shallow): Added keep_shallow INTEGER DEFAULT 0 column and migration to git_repositories table. Ingested repositories can now retain a persistent shallow copy (--depth 1) on disk under /app/data/repos/{repo_name} (on the mounted cache volume).
• Instant Full-File Resolution: file_reader.py reads unchunked source files directly from retained clones for instant inspection in Code Navigator, while incremental syncs utilize fast git fetch --depth 1 and git reset --hard.
• Full-Screen React Portals for Modals: Wrapped AddRepoModal, WebhookModal, and RepoSyncDrawer in createPortal(..., document.body) outside glassmorphism cards, preventing CSS containing-block clipping.

4. Comprehensive Documentation Sweep

• Updated README.md, DEVELOPER_DOCS.md, ARCHITECTURE.md, REQUIREMENTS.md, and VitePress user guides (docs/guide/user-guide/navigator.md, docs/guide/user-guide/git-repositories.md, docs/guide/index.md).
• Captured fresh, high-resolution desktop screenshots of all core UI views (Code Navigator, Git Repositories with shallow copy column, Add Repo Modal with shallow checkbox, Files & Storage, Search, Settings, Diagnostics, Overview).
• Updated verified test baselines: 522+ Pytest backend tests, 315 Vitest frontend tests across 32 suites.

Verification

• Frontend Unit & Component Tests: 315 passed (100% passing across 32 test files)
• Frontend Production Build: npm --prefix frontend run build passed cleanly
• Backend Test Suite: 522 passed, 2 skipped (100% passing)
• VitePress Documentation Build: npm run docs:build passed cleanly in 9.29s with 0 errors
• Live Chrome DevTools MCP Verification: Verified tree navigation, immediate Intelligence tab switching, and modal interactions