docs: Organize and archive implemented specs

Archive implemented specs to docs/specs/archive/:
- SPEC_15: Advanced Mode Performance (PR #65) - max_rounds=5, early termination
- SPEC_16: Unified Chat Client Architecture (PR #115) - HuggingFace + OpenAI factory
- SPEC_17: Accumulator Pattern (PR #117) - Fixes repr bug

Active specs remaining:
- SPEC_13: Evidence Deduplication (draft)
- SPEC_14: ClinicalTrials Outcomes (draft)

Add README.md index for specs folder.

docs/specs/README.md

@@ -0,0 +1,67 @@
+# Implementation Specs
+
+> Last updated: 2025-12-03
+>
+> **Note:** Implemented specs archived to `docs/specs/archive/`
+
+---
+
+## Active Specs (Not Yet Implemented)
+
+### SPEC_13: Evidence Deduplication
+
+**File:** `SPEC_13_EVIDENCE_DEDUPLICATION.md`
+**Status:** Draft - Ready for Implementation
+**Priority:** P1
+**GitHub Issue:** #94
+
+**Problem:** Same paper appears 2-3 times because Europe PMC and OpenAlex both index PubMed.
+
+**Solution:** Extract PMID from OpenAlex metadata, deduplicate by paper ID in SearchHandler.
+
+---
+
+### SPEC_14: ClinicalTrials Outcomes
+
+**File:** `SPEC_14_CLINICALTRIALS_OUTCOMES.md`
+**Status:** Draft - Ready for Implementation
+**Priority:** P1
+**GitHub Issue:** #95
+
+**Problem:** ClinicalTrials tool misses critical efficacy data (primary outcomes, results availability).
+
+**Solution:** Add `OutcomesModule` and `HasResults` to API fields, extract outcome measures.
+
+---
+
+## Implemented Specs (Archived)
+
+All implemented specs are in `docs/specs/archive/`. Summary:
+
+| Spec | Description | PR/Commit |
+|------|-------------|-----------|
+| SPEC_01 | Demo Termination | Archived |
+| SPEC_02 | E2E Testing | Archived |
+| SPEC_03 | OpenAlex Integration | Archived |
+| SPEC_04 | Magentic UX | Archived |
+| SPEC_05 | Orchestrator Cleanup | Archived |
+| SPEC_06 | Simple Mode Synthesis | Archived (deleted simple.py) |
+| SPEC_07 | LangGraph Memory Arch | Archived |
+| SPEC_08 | Integrate Memory Layer | Archived |
+| SPEC_09 | LlamaIndex Integration | Archived |
+| SPEC_10 | Domain Agnostic Refactor | Archived |
+| SPEC_11 | Sexual Health Focus | Archived |
+| SPEC_12 | Narrative Synthesis | Archived |
+| **SPEC_15** | Advanced Mode Performance | PR #65 - max_rounds=5, early termination |
+| **SPEC_16** | Unified Chat Client Architecture | PR #115 - HuggingFace + OpenAI factory |
+| **SPEC_17** | Accumulator Pattern | PR #117 - Fixes repr bug |
+
+---
+
+## How to Write a Spec
+
+1. Create `docs/specs/SPEC_{N}_{NAME}.md`
+2. Include: Problem, Solution, Test Plan, Acceptance Criteria
+3. Link to GitHub issue
+4. Update this README
+5. When implemented, move to `archive/`