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META_PLAN: DeepBoner Stabilization Roadmap

Created: 2025-12-03 Updated: 2025-12-04 Status: ✅ COMPLETE Purpose: Single source of truth for what to do next before adding features

Executive Summary

Codebase Health: PRODUCTION-READY

  • 302 tests passing
  • No type errors (mypy clean)
  • No linting issues (ruff clean)
  • All P3 tech debt resolved

Key Finding: Architecture is sound. All specs implemented. Tech debt cleaned.

Status: Steps 1-3 COMPLETE. Ready for feature development or documentation polish.

Current State Assessment

Documentation Status

Document Status Action
docs/STATUS_LLAMAINDEX_INTEGRATION.md DONE Keep as-is
docs/specs/archive/SPEC_13_EVIDENCE_DEDUPLICATION.md ✅ IMPLEMENTED Archived
docs/specs/archive/SPEC_14_CLINICALTRIALS_OUTCOMES.md ✅ IMPLEMENTED Archived
docs/future-roadmap/TOOL_ANALYSIS_CRITICAL.md ANALYSIS DONE Reference for future
docs/ARCHITECTURE.md PARTIAL Expand with diagrams
docs/architecture/system_registry.md DONE Canonical SSOT for wiring

Architecture Status

Component Status Notes
src/orchestrators/ COMPLETE Factory pattern, protocols
src/clients/ COMPLETE OpenAI/HuggingFace working, Provider Registry pattern
src/tools/ COMPLETE Deduplication + outcomes extraction done
src/agents/ FUNCTIONAL All agents wired, some experimental
src/services/ COMPLETE Embeddings, RAG, memory all working

Open Issues

Issue Priority Effort
Evidence deduplication (SPEC_13) HIGH ✅ DONE
ClinicalTrials outcomes (SPEC_14) HIGH ✅ DONE
Remove Anthropic wiring (P3) P3 ✅ DONE (PR #130)
Remove Modal wiring (P3) P3 ✅ DONE (PR #130)
Expand ARCHITECTURE.md LOW 2 hours
P3 Progress Bar positioning P3 30 min

The Next 5 Steps

Step 1: Implement SPEC_13 - Evidence Deduplication ✅ COMPLETE

Priority: HIGH DONE | Effort: 3-4 hours | Impact: 30-50% token savings

✅ COMPLETED - Deduplication now removes duplicate papers from PubMed/Europe PMC/OpenAlex.

Files modified:

  • src/tools/search_handler.py - Added extract_paper_id() and deduplicate_evidence()
  • src/tools/openalex.py - Extracts PMID from work.ids.pmid
  • tests/unit/tools/test_search_handler.py - 22 dedup tests
  • tests/integration/test_search_deduplication.py - Integration test

Spec: docs/specs/archive/SPEC_13_EVIDENCE_DEDUPLICATION.md (Status: Implemented)

Step 2: Implement SPEC_14 - ClinicalTrials Outcomes ✅ COMPLETE

Priority: HIGH DONE | Effort: 2-3 hours | Impact: Critical efficacy data

✅ COMPLETED - ClinicalTrials now extracts outcome measures and results status.

Files modified:

  • src/tools/clinicaltrials.py - Added OutcomesModule, HasResults fields, _extract_primary_outcome()
  • tests/unit/tools/test_clinicaltrials.py - 4 outcome tests + 2 integration tests

Spec: docs/specs/archive/SPEC_14_CLINICALTRIALS_OUTCOMES.md (Status: Implemented)

Step 3: Remove Anthropic + Modal Tech Debt ✅ COMPLETE

Priority: P3 DONE | Effort: 1 hour | Impact: Code clarity

✅ COMPLETED - Both Anthropic and Modal partial integrations removed in PR #130.

Files removed/modified:

  • src/utils/llm_factory.py - DELETED
  • src/tools/code_execution.py - DELETED
  • src/services/statistical_analyzer.py - DELETED
  • src/agents/analysis_agent.py, code_executor_agent.py - DELETED
  • All config, factory, and agent files cleaned

Docs archived: docs/bugs/archive/P3_REMOVE_ANTHROPIC_PARTIAL_WIRING.md, P3_MODAL_INTEGRATION_REMOVAL.md

Step 4: Documentation Consolidation

Priority: MEDIUM | Effort: 2 hours | Impact: Developer clarity

Create single canonical architecture doc with:

  • System flow diagram
  • Component interaction map
  • Error handling patterns
  • Deployment topology

Output: Expanded docs/ARCHITECTURE.md

Step 5: Create Implementation Status Matrix

Priority: LOW | Effort: 1 hour | Impact: Project tracking

Update docs/index.md or create docs/IMPLEMENTATION_STATUS.md with:

  • Phase completion tracking (14 phases)
  • Post-hackathon roadmap status
  • Clear DONE vs TODO markers

What NOT To Do (Yet)

  1. Add new features - Stabilize first
  2. Add new LLM providers - OpenAI/HuggingFace cover all use cases
  3. Build Neo4j knowledge graph - Overkill for current needs
  4. Implement full-text retrieval - Phase 15+ (after stabilization)
  5. Add MeSH term expansion - Phase 15+ (optimization)

Documentation Sprawl Analysis

Total docs: 91 markdown files in docs/

Organization:

docs/
├── architecture/      # Canonical architecture docs (4 files)
├── brainstorming/     # Ideas, not commitments (6 files)
├── bugs/              # Active bugs + archive (25+ files)
├── decisions/         # ADRs from Nov 2025 (2 files)
├── development/       # Dev guides (1 file)
├── future-roadmap/    # Deferred work (5 files)
├── guides/            # User guides (1 file)
├── implementation/    # Phase docs 1-14 (15 files)
├── specs/             # Feature specs (4 files)
├── ARCHITECTURE.md    # High-level overview
└── index.md           # Entry point

Recommendation: Structure is fine. Both SPEC_13 and SPEC_14 are now implemented.

Success Criteria

After completing Steps 1-5:

  • Evidence deduplication reduces duplicate papers by 80%+ ✅
  • ClinicalTrials shows outcome measures and results status ✅
  • No Anthropic references in codebase ✅ (PR #130)
  • No Modal references in codebase ✅ (PR #130)
  • ARCHITECTURE.md has flow diagrams (optional)
  • All 14 implementation phases marked DONE/TODO (optional)

Decision Log

Date Decision Rationale
2025-12-03 Implement specs before doc cleanup Specs are ready, high impact
2025-12-03 Remove Anthropic over adding Gemini Tech debt cleanup > new features
2025-12-03 Defer full-text retrieval Stabilize core first
2025-12-03 Mark SPEC_13 complete All acceptance criteria verified, PR #122
2025-12-03 Mark SPEC_14 complete All acceptance criteria verified (was already implemented)

References

  • docs/architecture/system_registry.md - Decorator/marker/tool wiring SSOT
  • docs/bugs/ACTIVE_BUGS.md - Current bug tracking
  • CLAUDE.md - Development commands and patterns