Organize markdown files into docs/ and notes/

Organizational change: Move markdown documentation from root to structured
directories for better project organization.

Files kept in root (2):
- README.md - Main project documentation
- CLAUDE.md - AI assistant instructions

Files moved to docs/ (3 new + existing):
- FILTER_TESTING_GUIDE.md
- QUICK_START.md
- UMAP_QUICK_START.md
+ Added docs/README.md index

Files moved to notes/ (16 new):
Development notes, implementation summaries, and reports:
- COMMUNITY_MECH_PLAN.md
- FINAL_SUMMARY.md
- GROWTH_MEDIA_FEATURE.md
- IMPLEMENTATION_SUMMARY.md
- NETWORK_CURATION_REPORT.md
- PHASE_1_COMPLETION.md through PHASE_5_COMPLETION.md
- PROJECT_COMPLETION_SUMMARY.md
- PR_DESCRIPTION.md
- PR_REVIEW_FIXES_SUMMARY.md
- UMAP_FILTER_IMPLEMENTATION.md
- UMAP_FINAL_SUMMARY.md
- UMAP_IMPLEMENTATION_SUMMARY.md
+ Added notes/README.md index

Rationale:
- docs/ contains user-facing guides and documentation
- notes/ contains development history and working documents
- Root directory is now cleaner with only essential files

Author: realmarcin

FILTER_TESTING_GUIDE.md docs/FILTER_TESTING_GUIDE.mdFILTER_TESTING_GUIDE.md renamed to docs/FILTER_TESTING_GUIDE.md

@@ -0,0 +1,39 @@
+# Documentation
+
+This directory contains user-facing documentation and guides for the CommunityMech knowledge base.
+
+## User Guides
+
+### Getting Started
+- **QUICK_START.md** - Quick start guide for using CommunityMech
+- **UMAP_QUICK_START.md** - Quick start guide for UMAP visualization
+
+### Feature Guides
+- **FILTER_TESTING_GUIDE.md** - Testing guide for filter panel functionality
+- **GROWTH_MEDIA_GUIDE.md** - Guide for growth media metadata
+- **UMAP_VISUALIZATION.md** - UMAP visualization documentation
+- **UMAP_COLOR_GUIDE.md** - Color scheme guide for UMAP plots
+
+### Curation & Quality
+- **NETWORK_QUALITY_GUIDE.md** - Network quality assurance guide
+- **NETWORK_REPAIR_USER_GUIDE.md** - User guide for network repair tools
+- **CURATION_PROGRESS_REPORT.md** - Community curation progress
+- **CULTUREMECH_MAPPING_GUIDE.md** - CultureMech mapping guide
+
+### Automation & Tools
+- **AUTOMATION_TOOLS.md** - Automation tools documentation
+- **LLM_SETUP_GUIDE.md** - LLM-assisted curation setup
+- **LLM_REPAIR_ROADMAP.md** - Roadmap for LLM repair capabilities
+- **pdf_fetching_capability.md** - PDF fetching feature documentation
+
+## Main Project Documentation
+
+See **../README.md** in the project root for:
+- Project overview and architecture
+- Installation and setup instructions
+- Core commands and workflows
+- LinkML schema documentation
+
+## Developer Instructions
+
+See **../CLAUDE.md** for AI assistant instructions and project conventions.