Refactor analysis sandbox with document VFS and expanded search

[ggozad]

Added

• Document virtual filesystem in analysis sandbox: Documents mounted at /documents/{id}/ with metadata.json (eager), content.txt (lazy), and items.jsonl (lazy). Standard Python pathlib.Path for browsing and reading document content and structure.
• execute_code skill tool: Direct code execution in the sandbox, surfaced as individual AG-UI events in the chat TUI. Items VFS uses a lazy bulk cache (~1s for 1000 documents vs 60s+ per-document queries).
• cite skill tool: Explicit citation registration with per-turn tracking via citation_index and citations fields in state
• --skill flag for chat TUI: haiku-rag chat -s rag -s analysis to enable specific skills
• --model overrides all agents: Chat, QA, research, and analysis agents all use the specified model
• Collapsible program display in chat TUI: Analysis code execution results shown as expandable code blocks

Changed

• BREAKING: Flatten skill architecture: Skill sub-agents now call search, execute_code, cite, list_documents, get_document directly — every tool call surfaces as an AG-UI event. Removes the 3rd agent layer where ask/analyze/research spawned inner agents whose tool calls were invisible.
• BREAKING: Rename RLM agent to analysis agent throughout:
  • agents/rlm/ → agents/analysis/, all classes renamed (RLMResult → AnalysisResult, etc.)
  • client.rlm() → client.analyze()
  • CLI: haiku-rag rlm → haiku-rag analyze
  • MCP: rlm_question → analyze
  • Config: rlm: → analysis: in YAML, RLMConfig → AnalysisConfig
  • Skill entrypoint: rag-rlm → rag-analysis
• Analysis sandbox search() returns expanded results with doc_item_refs and labels for cross-referencing with items.jsonl
• list_documents skill tool takes no parameters — returns all documents
• Per-turn citation tracking: citation_index: dict[str, Citation] (deduplicated) + citations: list[list[str]] (per-turn chunk IDs) replaces flat citation list
• Search rate limiting: Skill search tool enforces config.qa.max_searches
• Context expansion respects section boundaries: Sections within the char budget are returned whole regardless of item count. Too-large sections expand bounded by section edges. Adjacent sections no longer merge — only overlapping ranges do.
• Visualization shows full expanded section: visualize_chunk expands context before resolving bounding boxes, so all pages the section spans get highlighted.

Removed

• ask skill tool: Replaced by direct search + cite — the skill sub-agent searches and answers directly
• analyze skill tool: Replaced by direct execute_code + search + cite
• research skill tool: Removed from skill layer (still available via CLI haiku-rag research and MCP)
• get_document(), get_docling_document(): Removed from analysis sandbox — replaced by VFS
• get_chunk(): Removed from analysis sandbox — search results include expanded context
• create_analysis_toolset(): Removed unused tools/analysis.py module
• qa_history, reports from skill state: Conversational context handled by the outer chat agent
• combine_filters, build_document_filter: Removed from public API
• max_context_items: Removed from SearchConfig — max_context_chars is the sole expansion constraint
• QAHistoryEntry, tools/qa.py: Removed unused QA history model and relevance threshold

[codecov]

Codecov Report

❌ Patch coverage is 96.88474% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 91.78%. Comparing base (1049586) to head (8e555ab).
⚠️ Report is 25 commits behind head on main.

Files with missing lines	Patch %	Lines
...slim/haiku/rag/store/repositories/document_item.py	73.68%	5 Missing ⚠️
haiku_rag_slim/haiku/rag/mcp.py	33.33%	2 Missing ⚠️
...aiku_rag_slim/haiku/rag/agents/analysis/sandbox.py	99.27%	1 Missing ⚠️
haiku_rag_slim/haiku/rag/client.py	95.65%	1 Missing ⚠️
..._rag_slim/haiku/rag/store/repositories/document.py	83.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #342      +/-   ##
==========================================
- Coverage   92.18%   91.78%   -0.41%     
==========================================
  Files          75       73       -2     
  Lines        3954     3942      -12     
==========================================
- Hits         3645     3618      -27     
- Misses        309      324      +15     

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