diff --git a/.claude/commands/check-db.md b/.claude/commands/check-db.md
new file mode 100644
index 0000000..2da92e2
--- /dev/null
+++ b/.claude/commands/check-db.md
@@ -0,0 +1,29 @@
+---
+description: Verify RootsMagic database file exists and is accessible
+---
+
+Check that the RootsMagic database file is present and can be queried.
+
+```bash
+DB_PATH="${RM_DATABASE_PATH:-data/Iiams.rmtree}"
+
+if [ ! -f "$DB_PATH" ]; then
+  echo "❌ Database file not found: $DB_PATH"
+  echo ""
+  echo "Set RM_DATABASE_PATH in config/.env"
+  exit 1
+fi
+
+echo "✅ Database found: $DB_PATH"
+echo ""
+
+# Get basic stats
+PERSON_COUNT=$(sqlite3 "$DB_PATH" "SELECT COUNT(*) FROM PersonTable;")
+EVENT_COUNT=$(sqlite3 "$DB_PATH" "SELECT COUNT(*) FROM EventTable;")
+SOURCE_COUNT=$(sqlite3 "$DB_PATH" "SELECT COUNT(*) FROM SourceTable;")
+
+echo "📊 Database Statistics:"
+echo "  • Persons: $PERSON_COUNT"
+echo "  • Events: $EVENT_COUNT"
+echo "  • Sources: $SOURCE_COUNT"
+```
diff --git a/.claude/commands/coverage.md b/.claude/commands/coverage.md
new file mode 100644
index 0000000..1dd5556
--- /dev/null
+++ b/.claude/commands/coverage.md
@@ -0,0 +1,11 @@
+---
+description: Run tests with coverage report
+---
+
+Run the full test suite with coverage analysis. Shows which lines are covered and identifies gaps.
+
+```bash
+uv run pytest --cov=rmagent --cov-report=term-missing --cov-report=html
+echo ""
+echo "📊 Coverage report generated at: file://$(pwd)/htmlcov/index.html"
+```
diff --git a/.claude/commands/doc-review.md b/.claude/commands/doc-review.md
new file mode 100644
index 0000000..cdac1df
--- /dev/null
+++ b/.claude/commands/doc-review.md
@@ -0,0 +1,149 @@
+---
+description: Review documentation for accuracy and completeness
+show-prompt: true
+meta: true
+---
+
+Review project documentation to ensure it's concise, current, and accurate.
+
+**Modes:**
+- `/doc-review` or `/doc-review brief` - Review root docs and INDEX.md
+- `/doc-review deep` - Review ALL documentation files
+
+This command reads documentation files and asks the LLM to verify:
+1. Content is concise and well-organized
+2. Information is current (no outdated references)
+3. Cross-references and links are accurate
+4. No contradictions between documents
+5. INDEX.md accurately reflects documentation structure
+
+```bash
+MODE="${1:-brief}"
+
+if [ "$MODE" = "deep" ]; then
+  cat <<'PROMPT'
+Please perform a DEEP documentation review of the RMAgent project.
+
+Review ALL documentation files for:
+1. **Accuracy** - Are all statements, commands, and examples correct?
+2. **Currency** - Is information up-to-date? Any outdated references?
+3. **Consistency** - Do documents contradict each other?
+4. **Completeness** - Are there gaps in documentation coverage?
+5. **Conciseness** - Can any content be condensed without losing value?
+6. **Organization** - Is content in the right location?
+
+**Root Documentation Files:**
+PROMPT
+
+  echo ""
+  echo "=== CLAUDE.md ==="
+  head -100 CLAUDE.md
+  echo ""
+  echo "=== README.md ==="
+  head -100 README.md
+  echo ""
+  echo "=== AGENTS.md ==="
+  head -50 AGENTS.md
+  echo ""
+  echo "=== CONTRIBUTING.md ==="
+  head -50 CONTRIBUTING.md
+  echo ""
+  echo "=== CHANGELOG.md ==="
+  head -30 CHANGELOG.md
+
+  cat <<'PROMPT'
+
+**Documentation Index:**
+PROMPT
+
+  echo ""
+  echo "=== docs/INDEX.md ==="
+  cat docs/INDEX.md
+
+  cat <<'PROMPT'
+
+**All Documentation Files:**
+PROMPT
+
+  echo ""
+  find docs -name "*.md" -type f | sort | while read file; do
+    echo ""
+    echo "=== $file ==="
+    head -80 "$file"
+    echo "... [file continues]"
+  done
+
+  cat <<'PROMPT'
+
+Please provide:
+1. **Overall Assessment** - General state of documentation
+2. **Critical Issues** - Must-fix problems (inaccuracies, broken links, outdated info)
+3. **Recommendations** - Suggestions for improvement
+4. **Specific Fixes** - Line-by-line corrections needed
+
+Focus on actionable feedback that improves documentation quality.
+PROMPT
+
+else
+  # Brief mode - just check root docs + INDEX.md
+  cat <<'PROMPT'
+Please perform a BRIEF documentation review of the RMAgent project's core files.
+
+Review the following files for:
+1. **Accuracy** - Are statements, commands, and statistics correct?
+2. **Currency** - Any outdated references or old information?
+3. **Consistency** - Do these files contradict each other?
+4. **Conciseness** - Is content appropriately detailed (not too verbose)?
+5. **INDEX.md Accuracy** - Does INDEX.md correctly reference all docs in the repository?
+
+**Root Documentation Files:**
+PROMPT
+
+  echo ""
+  echo "=== CLAUDE.md ==="
+  cat CLAUDE.md
+  echo ""
+  echo "=== README.md ==="
+  cat README.md
+  echo ""
+  echo "=== AGENTS.md ==="
+  cat AGENTS.md
+  echo ""
+  echo "=== CONTRIBUTING.md ==="
+  cat CONTRIBUTING.md
+  echo ""
+  echo "=== CHANGELOG.md ==="
+  cat CHANGELOG.md
+
+  cat <<'PROMPT'
+
+**Documentation Index:**
+PROMPT
+
+  echo ""
+  echo "=== docs/INDEX.md ==="
+  cat docs/INDEX.md
+
+  cat <<'PROMPT'
+
+**Verify INDEX.md Completeness:**
+Check that docs/INDEX.md accurately references all documentation files in the repository.
+PROMPT
+
+  echo ""
+  echo "=== All docs files in repository ==="
+  find docs -name "*.md" -type f | sort
+
+  cat <<'PROMPT'
+
+Please provide:
+1. **Quick Assessment** - Overall state of core documentation
+2. **Critical Issues** - Any inaccuracies, broken references, or outdated info
+3. **INDEX.md Status** - Is it complete and accurate?
+4. **Quick Wins** - Easy improvements to make immediately
+
+Be concise and actionable. Focus on what needs fixing right now.
+PROMPT
+
+fi
+```
diff --git a/.claude/commands/docs.md b/.claude/commands/docs.md
new file mode 100644
index 0000000..420d3c9
--- /dev/null
+++ b/.claude/commands/docs.md
@@ -0,0 +1,33 @@
+---
+description: Open documentation in browser or show quick reference
+---
+
+Quick access to RMAgent documentation.
+
+Usage:
+- `/docs` - Show documentation index
+- `/docs schema` - Open schema reference
+- `/docs data-formats` - Open data formats reference
+- `/docs dev` - Open developer guide
+
+```bash
+case "$ARGUMENTS" in
+  schema)
+    echo "📖 Schema Reference: docs/reference/schema/schema-reference.md"
+    cat docs/reference/schema/schema-reference.md | head -50
+    ;;
+  data-formats)
+    echo "📖 Data Formats: docs/reference/data-formats/"
+    ls -1 docs/reference/data-formats/
+    ;;
+  dev)
+    echo "📖 Developer Guide: docs/guides/developer-guide.md"
+    cat docs/guides/developer-guide.md | head -50
+    ;;
+  *)
+    echo "📚 RMAgent Documentation Index"
+    echo ""
+    cat docs/INDEX.md | head -80
+    ;;
+esac
+```
diff --git a/.claude/commands/lint.md b/.claude/commands/lint.md
new file mode 100644
index 0000000..d13d387
--- /dev/null
+++ b/.claude/commands/lint.md
@@ -0,0 +1,22 @@
+---
+description: Run linting checks (ruff and black)
+---
+
+Run code quality checks using ruff and black formatters.
+
+Usage:
+- `/lint` - Check code without modifying
+- `/lint fix` - Auto-fix issues where possible
+
+```bash
+if [ "$ARGUMENTS" = "fix" ]; then
+  echo "🔧 Auto-fixing issues..."
+  uv run ruff check --fix .
+  uv run black .
+  echo "✅ Fixes applied"
+else
+  echo "🔍 Checking code quality..."
+  uv run ruff check .
+  uv run black --check .
+fi
+```
diff --git a/.claude/commands/rm-ask.md b/.claude/commands/rm-ask.md
new file mode 100644
index 0000000..e628a91
--- /dev/null
+++ b/.claude/commands/rm-ask.md
@@ -0,0 +1,23 @@
+---
+description: Ask a question about the genealogy database using AI
+show-prompt: true
+meta: true
+---
+
+Ask natural language questions about your genealogy data. Uses AI to query and analyze the database.
+
+Usage:
+- `/rm-ask "Who are the ancestors of John Smith?"`
+- `/rm-ask "Find everyone born in Baltimore"`
+- `/rm-ask "Show family relationships for person 1"`
+
+```bash
+if [ -z "$ARGUMENTS" ]; then
+  echo "❌ Error: Question required"
+  echo "Usage: /rm-ask \"Your question here\""
+  exit 1
+fi
+
+echo "🤔 Asking AI about your genealogy data..."
+uv run rmagent ask "$ARGUMENTS"
+```
diff --git a/.claude/commands/rm-bio.md b/.claude/commands/rm-bio.md
new file mode 100644
index 0000000..3d1a3be
--- /dev/null
+++ b/.claude/commands/rm-bio.md
@@ -0,0 +1,27 @@
+---
+description: Generate a biography for a person using rmagent
+show-prompt: true
+meta: true
+---
+
+Generate a biography using the rmagent CLI. Requires a person ID.
+
+Usage:
+- `/rm-bio 1` - Generate standard biography for person 1
+- `/rm-bio 1 short` - Generate short biography
+- `/rm-bio 1 comprehensive` - Generate comprehensive biography
+
+```bash
+if [ -z "$1" ]; then
+  echo "❌ Error: Person ID required"
+  echo "Usage: /rm-bio <person_id> [length]"
+  echo "Example: /rm-bio 1 standard"
+  exit 1
+fi
+
+PERSON_ID=$1
+LENGTH=${2:-standard}
+
+echo "📝 Generating $LENGTH biography for person $PERSON_ID..."
+uv run rmagent bio $PERSON_ID --length $LENGTH --output reports/biographies/
+```
diff --git a/.claude/commands/rm-person.md b/.claude/commands/rm-person.md
new file mode 100644
index 0000000..a980dc5
--- /dev/null
+++ b/.claude/commands/rm-person.md
@@ -0,0 +1,23 @@
+---
+description: Query person details from RootsMagic database
+---
+
+Query detailed information about a person using rmagent CLI.
+
+Usage:
+- `/rm-person 1` - Basic person info
+- `/rm-person 1 --events` - Include all events
+- `/rm-person 1 --family` - Include family relationships
+- `/rm-person 1 --ancestors` - Include ancestors
+- `/rm-person 1 --descendants` - Include descendants
+
+```bash
+if [ -z "$1" ]; then
+  echo "❌ Error: Person ID required"
+  echo "Usage: /rm-person <person_id> [--options]"
+  exit 1
+fi
+
+echo "👤 Querying person $1..."
+uv run rmagent person $@
+```
diff --git a/.claude/commands/rm-quality.md b/.claude/commands/rm-quality.md
new file mode 100644
index 0000000..d47b57f
--- /dev/null
+++ b/.claude/commands/rm-quality.md
@@ -0,0 +1,22 @@
+---
+description: Run data quality validation on RootsMagic database
+---
+
+Run data quality checks on the RootsMagic database.
+
+Usage:
+- `/rm-quality` - Run all quality checks
+- `/rm-quality dates` - Check only date issues
+- `/rm-quality names` - Check only name issues
+- `/rm-quality places` - Check only place issues
+- `/rm-quality relationships` - Check only relationship issues
+
+```bash
+if [ -z "$ARGUMENTS" ]; then
+  echo "🔍 Running all data quality checks..."
+  uv run rmagent quality --format table
+else
+  echo "🔍 Running quality checks for category: $ARGUMENTS"
+  uv run rmagent quality --category $ARGUMENTS --format table
+fi
+```
diff --git a/.claude/commands/rm-search.md b/.claude/commands/rm-search.md
new file mode 100644
index 0000000..6d1681b
--- /dev/null
+++ b/.claude/commands/rm-search.md
@@ -0,0 +1,21 @@
+---
+description: Search RootsMagic database by name or place
+---
+
+Search the RootsMagic database for people by name or place.
+
+Usage:
+- `/rm-search --name "John Smith"` - Search by name
+- `/rm-search --place "Baltimore"` - Search by place
+- `/rm-search --name "Smith" --limit 10` - Limit results
+
+```bash
+if [ -z "$ARGUMENTS" ]; then
+  echo "❌ Error: Search parameters required"
+  echo "Usage: /rm-search --name \"Name\" or /rm-search --place \"Place\""
+  exit 1
+fi
+
+echo "🔎 Searching database..."
+uv run rmagent search $ARGUMENTS
+```
diff --git a/.claude/commands/rm-timeline.md b/.claude/commands/rm-timeline.md
new file mode 100644
index 0000000..9600c66
--- /dev/null
+++ b/.claude/commands/rm-timeline.md
@@ -0,0 +1,22 @@
+---
+description: Generate timeline visualization for a person
+---
+
+Generate a TimelineJS3 timeline for a person's life events.
+
+Usage:
+- `/rm-timeline 1` - Generate JSON timeline for person 1
+- `/rm-timeline 1 --format html` - Generate HTML timeline
+- `/rm-timeline 1 --include-family` - Include family events
+- `/rm-timeline 1 --group-by-phase` - Group events by life phases
+
+```bash
+if [ -z "$1" ]; then
+  echo "❌ Error: Person ID required"
+  echo "Usage: /rm-timeline <person_id> [options]"
+  exit 1
+fi
+
+echo "📅 Generating timeline for person $1..."
+uv run rmagent timeline $@
+```
diff --git a/.claude/commands/test.md b/.claude/commands/test.md
new file mode 100644
index 0000000..a6088f5
--- /dev/null
+++ b/.claude/commands/test.md
@@ -0,0 +1,19 @@
+---
+description: Run pytest tests with optional filters
+---
+
+Run the test suite using pytest. You can optionally specify a test file or pattern.
+
+Usage:
+- `/test` - Run all tests
+- `/test unit` - Run only unit tests
+- `/test integration` - Run only integration tests
+- `/test test_queries.py` - Run specific test file
+
+```bash
+if [ -z "$ARGUMENTS" ]; then
+  uv run pytest -v
+else
+  uv run pytest -v tests/$ARGUMENTS*
+fi
+```
diff --git a/CLAUDE.md b/CLAUDE.md
index 3261928..c54266a 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -24,40 +24,45 @@ rmagent/
 │   └── rmlib/                # Core library (database, parsers, queries)
 ├── config/                   # Runtime config (config/.env)
 ├── data/                     # Database files (*.rmtree, NOT tracked in git)
-├── data_reference/           # 18 schema/format docs (RM11_*.md)
-├── docs/                     # Project docs (AI_AGENT_TODO.md, USER_GUIDE.md, MVP_CHECKPOINT.md)
+├── docs/                     # **📚 START HERE: docs/INDEX.md** - Complete documentation
+│   ├── INDEX.md             # Master table of contents
+│   ├── getting-started/     # Installation, quickstart, configuration
+│   ├── guides/              # User & developer guides
+│   ├── reference/           # Schema, formats, query patterns
+│   ├── projects/            # Active feature development
+│   └── archive/             # Completed milestones & summaries
 ├── sqlite-extension/         # ICU extension for RMNOCASE collation
-└── tests/unit/               # Test suite (245+ tests, pytest)
+└── tests/unit/               # Test suite (490+ tests, pytest)
 ```
 
-## Essential Documentation (data_reference/)
+## 📚 Essential Documentation
 
-**Schema & Structure:**
-- **RM11_Schema_Reference.md** - START HERE: tables, fields, relationships, query patterns
-- **RM11_schema_annotated.sql** - SQL with comments for query writing
-- **RM11_DataDef.yaml** - Field enumerations and constraints
+**For complete documentation, see [`docs/INDEX.md`](docs/INDEX.md)**
 
-**Core Formats:**
-- **RM11_Date_Format.md** - CRITICAL: 24-char date encoding (ranges, qualifiers, BC/AD)
-- **RM11_Place_Format.md** - Comma-delimited hierarchy (City, County, State, Country)
-- **RM11_FactTypes.md** - 65 built-in event types
+### Quick Reference (Most Important Files)
 
-**BLOB Structures (UTF-8 XML with BOM):**
-- **RM11_BLOB_SourceFields.md** - SourceTable.Fields extraction
-- **RM11_BLOB_SourceTemplateFieldDefs.md** - Template definitions (433 templates)
-- **RM11_BLOB_CitationFields.md** - CitationTable.Fields extraction
+**Schema & Database:**
+- **[schema-reference.md](docs/reference/schema/schema-reference.md)** - START HERE: tables, fields, relationships
+- **[annotated-schema.sql](docs/reference/schema/annotated-schema.sql)** - SQL with comments
+- **[data-definitions.yaml](docs/reference/schema/data-definitions.yaml)** - Field enumerations
 
-**Data Quality & Output:**
-- **RM11_Data_Quality_Rules.md** - 24 validation rules across 6 categories
-- **RM11_Query_Patterns.md** - 15 optimized SQL patterns
-- **RM11_Biography_Best_Practices.md** - 9-section structure, citation styles
-- **RM11_Timeline_Construction.md** - TimelineJS3 JSON generation
+**Critical Data Formats:**
+- **[date-format.md](docs/reference/data-formats/date-format.md)** - ⚠️ CRITICAL: 24-char date encoding
+- **[place-format.md](docs/reference/data-formats/place-format.md)** - Comma-delimited hierarchy
+- **[fact-types.md](docs/reference/data-formats/fact-types.md)** - 65 built-in event types
 
-**Additional References:**
-- RM11_Relationships.md (Relate1/Relate2 calculations)
-- RM11_Name_Display_Logic.md (context-aware name selection)
-- RM11_EventTable_Details.md (Details field patterns)
-- RM11_Sentence_Templates.md (reference only - AI generates text natively)
+**BLOB Parsing (UTF-8 XML with BOM):**
+- **[blob-source-fields.md](docs/reference/data-formats/blob-source-fields.md)** - SourceTable.Fields
+- **[blob-citation-fields.md](docs/reference/data-formats/blob-citation-fields.md)** - CitationTable.Fields
+- **[blob-template-field-defs.md](docs/reference/data-formats/blob-template-field-defs.md)** - Template definitions
+
+**Query & Quality:**
+- **[query-patterns.md](docs/reference/query-patterns/query-patterns.md)** - 15 optimized SQL patterns
+- **[data-quality-rules.md](docs/reference/query-patterns/data-quality-rules.md)** - 24 validation rules
+
+**Biography & Output:**
+- **[biography-best-practices.md](docs/reference/biography/biography-best-practices.md)** - 9-section structure
+- **[timeline-construction.md](docs/reference/biography/timeline-construction.md)** - TimelineJS3 format
 
 ## Critical Schema Patterns
 
@@ -106,6 +111,26 @@ RM_DATABASE_PATH=data/Iiams.rmtree
 LOG_LEVEL=DEBUG                      # Enable LLM logging
 ```
 
+### Claude Code Integration
+
+RMAgent includes 12 custom slash commands and automated hooks for Claude Code:
+
+**Quick Commands:**
+- `/rm-bio <id>` - Generate biography with AI
+- `/rm-person <id>` - Query person from database
+- `/rm-quality` - Run data quality checks
+- `/doc-review [brief|deep]` - Review documentation for accuracy with AI
+- `/test` - Run pytest suite
+- `/coverage` - Run tests with coverage
+- `/check-db` - Verify database connection
+
+**Automated Hooks:**
+- Coverage reminders after pytest runs
+- Commit preview before git push
+- Documentation review reminder (pre-commit)
+
+**See [`docs/guides/claude-code-setup.md`](docs/guides/claude-code-setup.md) for complete setup and usage guide.**
+
 ## Project Status (2025-10-12)
 
 🎉 **Milestone 2: MVP ACHIEVED** - All foundation phases complete (33/33 tasks)
@@ -129,11 +154,11 @@ LOG_LEVEL=DEBUG                      # Enable LLM logging
 - Source formatting improvements (italic rendering, type prefix removal)
 - Biography collision handling with sequential numbering
 
-**Test Coverage:** 418 tests, 82% overall coverage (97% database, 96% parsers, 91% quality)
+**Test Coverage:** 490 tests, 88% overall coverage (97% database, 96% parsers, 94% rendering)
 
 **Next Phase:** Phase 7 - Production Polish (performance optimization, advanced features)
 
-See `docs/AI_AGENT_TODO.md` for complete roadmap.
+See [`docs/projects/ai-agent/roadmap.md`](docs/projects/ai-agent/roadmap.md) for complete roadmap.
 
 ## CLI Commands
 
@@ -159,7 +184,7 @@ All commands use `uv run rmagent [command]`:
 
 ## LangChain v1.0 Integration (Future)
 
-**Status:** Zero active LangChain imports. v1.0 upgrade planned for Phase 7. See `docs/RM11_LangChain_Upgrade.md` and `AGENTS.md` for patterns.
+**Status:** Zero active LangChain imports. v1.0 upgrade planned for Phase 7. See [`docs/projects/ai-agent/langchain-upgrade.md`](docs/projects/ai-agent/langchain-upgrade.md) for detailed plan.
 
 **v1.0 Requirements:** `create_agent()`, `system_prompt="string"`, TypedDict state only. New code goes in `rmagent/agent/lc/` directory.
 
@@ -205,7 +230,7 @@ All PRs automatically run:
 - Full test suite with coverage (must maintain 80%+)
 - See `.github/workflows/pr-tests.yml`
 
-**For detailed workflow instructions, see `docs/GIT_WORKFLOW_GUIDE.md`**
+**For detailed workflow instructions, see [`docs/guides/git-workflow.md`](docs/guides/git-workflow.md)**
 
 ## Quick Reference
 
diff --git a/README.md b/README.md
index 267c868..89883ec 100644
--- a/README.md
+++ b/README.md
@@ -132,7 +132,7 @@ quality_summary = agent.analyze_data_quality()
 ### CLI Setup Options
 
 **Option 1: Direct Access (Recommended)**
-Run `./setup_cli.sh` to enable direct CLI access and tab completion. See [docs/CLI_SETUP.md](docs/CLI_SETUP.md) for details.
+Run `./setup_cli.sh` to enable direct CLI access and tab completion.
 
 After setup, use commands directly:
 ```bash
@@ -377,13 +377,12 @@ When LangChain v1.0 stable releases, use these patterns:
 
 ### Migration Plan
 
-See `docs/RM11_LangChain_Upgrade.md` for complete upgrade strategy and timeline.
+See [`docs/projects/ai-agent/langchain-upgrade.md`](docs/projects/ai-agent/langchain-upgrade.md) for complete upgrade strategy and timeline.
 
 **Key Points:**
 - New LangChain code goes in `rmagent/agent/lc/` directory
 - Use v1.0 patterns from day one (no migration needed)
 - Maintain 80%+ test coverage for all LangChain features
-- See `AGENTS.md` for comprehensive best practices
 
 ## Development
 
@@ -414,33 +413,34 @@ uv run pytest --cov=rmagent --cov-report=html
 
 ## Documentation
 
-**📚 Complete Documentation Index:** [docs/README.md](docs/README.md)
+**📚 Complete Documentation Index:** **[docs/INDEX.md](docs/INDEX.md)** ← START HERE
 
 ### For New Users
 
-Start here to get up and running:
+Get up and running quickly:
 
-1. **[INSTALL.md](INSTALL.md)** - Installation guide (macOS, Linux, Windows/WSL2)
-2. **[CONFIGURATION.md](CONFIGURATION.md)** - Configuration, LLM providers, prompt customization
-3. **[USAGE.md](USAGE.md)** - Complete CLI reference with 50+ examples
-4. **[FAQ.md](FAQ.md)** - Common questions and troubleshooting
-
-**Comprehensive Guide:** [docs/USER_GUIDE.md](docs/USER_GUIDE.md) (31KB, all-in-one)
+1. **[Installation Guide](docs/getting-started/installation.md)** - Install RMAgent and dependencies
+2. **[Quick Start](docs/getting-started/quickstart.md)** - 5-minute tutorial
+3. **[Configuration Guide](docs/getting-started/configuration.md)** - Set up API keys and database
+4. **[User Guide](docs/guides/user-guide.md)** - Complete CLI reference with examples
+5. **[FAQ](docs/faq.md)** - Troubleshooting and common questions
 
 ### For Developers
 
-Start here to contribute or extend RMAgent:
+Contribute or extend RMAgent:
 
-1. **[DEVELOPER_GUIDE.md](DEVELOPER_GUIDE.md)** - Architecture, design patterns, API reference
+1. **[Developer Guide](docs/guides/developer-guide.md)** - Architecture, design patterns, API reference
 2. **[CONTRIBUTING.md](CONTRIBUTING.md)** - Contribution workflow and coding standards
-3. **[TESTING.md](TESTING.md)** - Testing guide (279 tests, coverage analysis)
-4. **[CHANGELOG.md](CHANGELOG.md)** - Complete version history
+3. **[Testing Guide](docs/guides/testing-guide.md)** - Testing guide (490 tests, 88% coverage)
+4. **[Git Workflow](docs/guides/git-workflow.md)** - Branching strategy and PR process
+5. **[CHANGELOG.md](CHANGELOG.md)** - Version history
 
-### Additional Documentation
+### Technical Reference
 
-- **[AGENTS.md](AGENTS.md)** - Agent design patterns
-- **[data_reference/](data_reference/)** - RootsMagic 11 schema (18 reference docs)
-- **[docs/](docs/)** - Project documentation and completion reports
+- **[Schema Reference](docs/reference/schema/)** - RootsMagic 11 database schema
+- **[Data Formats](docs/reference/data-formats/)** - Date/place/BLOB formats
+- **[Query Patterns](docs/reference/query-patterns/)** - Optimized SQL patterns
+- **[Biography Reference](docs/reference/biography/)** - Biography generation guidelines
 
 ## Status
 
@@ -450,7 +450,7 @@ Start here to contribute or extend RMAgent:
 **Completion:** All 26 foundation tasks complete (Phases 1-4)
 **Next Focus:** Testing & Quality improvements (Phase 5)
 
-See [docs/MVP_CHECKPOINT.md](docs/MVP_CHECKPOINT.md) for complete verification report.
+See [docs/archive/checkpoints/mvp-checkpoint.md](docs/archive/checkpoints/mvp-checkpoint.md) for complete verification report.
 
 ---
 
@@ -501,9 +501,9 @@ See [docs/MVP_CHECKPOINT.md](docs/MVP_CHECKPOINT.md) for complete verification r
 - ✅ Export Command (Hugo blog export with batch support, 8 tests, 74% coverage)
 - ✅ Search Command (name/place search with phonetic matching, 8 tests, 88% coverage)
 
-**⏭️ Next Tasks:** Phase 5 - Testing & Quality (comprehensive integration testing)
+**⏭️ Next Tasks:** Phase 7 - Production Polish (performance optimization, advanced features)
 
-See `docs/AI_AGENT_TODO.md` for detailed progress and roadmap.
+See [`docs/projects/ai-agent/roadmap.md`](docs/projects/ai-agent/roadmap.md) for detailed progress and roadmap.
 
 ## Repository
 
diff --git a/data/Iiams.rmtree-shm b/data/Iiams.rmtree-shm
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diff --git a/docs/INDEX.md b/docs/INDEX.md
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--- /dev/null
+++ b/docs/INDEX.md
@@ -0,0 +1,172 @@
+# RMAgent Documentation Index
+
+**Version**: 1.0
+**Last Updated**: 2025-10-15
+
+This is the master table of contents for all RMAgent documentation. All paths are relative to the `docs/` directory.
+
+---
+
+## Quick Links
+
+- [Installation Guide](getting-started/installation.md) - Get RMAgent installed
+- [Quick Start](getting-started/quickstart.md) - 5-minute getting started guide
+- [User Guide](guides/user-guide.md) - Complete CLI reference
+- [Developer Guide](guides/developer-guide.md) - Contributing and development setup
+- [FAQ](faq.md) - Frequently asked questions
+
+---
+
+## 📚 Documentation Structure
+
+### Getting Started
+
+New users start here:
+
+- **[installation.md](getting-started/installation.md)** - Installation instructions (uv, dependencies, database setup)
+- **[quickstart.md](getting-started/quickstart.md)** - 5-minute tutorial with first commands
+- **[configuration.md](getting-started/configuration.md)** - Environment configuration and API keys
+
+### User Guides
+
+Complete guides for using RMAgent:
+
+- **[user-guide.md](guides/user-guide.md)** - Complete CLI command reference and usage patterns
+- **[faq.md](faq.md)** - Frequently asked questions and troubleshooting
+
+### Developer Guides
+
+For contributors and developers:
+
+- **[developer-guide.md](guides/developer-guide.md)** - Architecture, coding standards, development setup
+- **[testing-guide.md](guides/testing-guide.md)** - Running tests, writing tests, coverage
+- **[git-workflow.md](guides/git-workflow.md)** - Branching strategy, commit conventions, PR process
+- **[claude-code-setup.md](guides/claude-code-setup.md)** - Claude Code slash commands and hooks configuration
+
+### Reference Documentation
+
+Technical reference materials:
+
+#### Schema & Database
+- **[reference/schema/](reference/schema/)** - RootsMagic 11 database schema documentation
+  - `schema-reference.md` - Complete table and field reference
+  - `annotated-schema.sql` - Annotated SQL schema
+  - `data-definitions.yaml` - Field enumerations and constraints
+  - `relationships.md` - Parent-child and family relationships
+
+#### Data Formats
+- **[reference/data-formats/](reference/data-formats/)** - RootsMagic data format specifications
+  - `date-format.md` - 24-character date encoding (CRITICAL)
+  - `place-format.md` - Comma-delimited place hierarchy
+  - `blob-fields.md` - UTF-8 XML BLOB parsing (sources, citations, templates)
+  - `fact-types.md` - 65 built-in event types
+
+#### Query Patterns
+- **[reference/query-patterns/](reference/query-patterns/)** - SQL query patterns and best practices
+  - `query-patterns.md` - 15 optimized query patterns
+  - `rmnocase-collation.md` - ICU extension for case-insensitive text matching
+  - `data-quality-rules.md` - 24 validation rules across 6 categories
+
+#### Biography
+- **[reference/biography/](reference/biography/)** - Biography generation reference
+  - `biography-best-practices.md` - 9-section structure, citation styles
+  - `timeline-construction.md` - TimelineJS3 JSON generation
+
+### Active Projects
+
+Point-in-time feature work and planning documents:
+
+#### AI Agent Development
+- **[projects/ai-agent/](projects/ai-agent/)**
+  - `roadmap.md` - AI agent development roadmap (phases 1-7)
+  - `langchain-upgrade.md` - LangChain 1.0 migration plan
+  - `multi-agent-plan.md` - Multi-agent architecture design
+
+#### Census Extraction
+- **[projects/census-extraction/](projects/census-extraction/)**
+  - `architecture.md` - Census extraction system architecture
+  - `implementation-plan.md` - Step-by-step implementation plan
+
+#### Biography & Citations
+- **[projects/biography-citations/](projects/biography-citations/)**
+  - `citation-implementation.md` - Citation processing implementation
+  - `married-name-search.md` - Married name search optimization
+
+### Archive
+
+Completed milestones and historical documentation:
+
+- **[archive/checkpoints/](archive/checkpoints/)** - Milestone completion documents
+  - `mvp-checkpoint.md` - MVP milestone (Phases 1-6 complete)
+  - `phase-5-completion.md` - Testing & quality phase
+  - `phase-6-completion.md` - Documentation phase
+
+- **[archive/summaries/](archive/summaries/)** - Implementation summaries
+  - `integration-testing-summary.md` - Integration test implementation
+  - `optimization-summary.md` - Performance optimization work
+  - `test-coverage-analysis.md` - Coverage improvement analysis
+
+### Root Documentation
+
+Key files in the repository root (not in docs/):
+
+- **[CLAUDE.md](../CLAUDE.md)** - AI assistant context and project guide
+- **[AGENTS.md](../AGENTS.md)** - LangChain patterns and multi-agent architecture
+- **[README.md](../README.md)** - Repository entry point and quick start
+- **[CONTRIBUTING.md](../CONTRIBUTING.md)** - Contribution guidelines
+- **[CHANGELOG.md](../CHANGELOG.md)** - Version history and release notes
+
+---
+
+## 🎯 For Claude Code and AI Assistants
+
+When working on this codebase:
+
+1. **Start with**: `CLAUDE.md` (root) for project context and guidelines
+2. **Schema questions**: `reference/schema/schema-reference.md`
+3. **Data parsing**: `reference/data-formats/` (especially `date-format.md`)
+4. **Query patterns**: `reference/query-patterns/query-patterns.md`
+5. **Active work**: `projects/` subdirectories for current feature development
+6. **Testing**: `guides/testing-guide.md`
+
+---
+
+## 📝 Documentation Maintenance
+
+### Keeping Docs Current
+
+- **Active work** → `projects/` (move to `archive/` when complete)
+- **Completed milestones** → `archive/checkpoints/`
+- **Implementation notes** → `archive/summaries/`
+- **Update INDEX.md** when adding/moving documentation
+
+### Naming Conventions
+
+- **Directories**: `lowercase-with-hyphens/`
+- **Files**: `lowercase-with-hyphens.md`
+- **Be descriptive**: `installation.md` not `install.md`
+- **No abbreviations** unless universally known (e.g., `faq.md` is OK)
+
+### Where Does It Go?
+
+| Content Type | Location | Example |
+|--------------|----------|---------|
+| User-facing guides | `guides/` | CLI reference, tutorials |
+| Installation/setup | `getting-started/` | Installation, configuration |
+| Technical reference | `reference/` | Schema, formats, patterns |
+| Active feature work | `projects/{feature}/` | Planning, architecture docs |
+| Completed work | `archive/` | Checkpoints, summaries |
+| General questions | `faq.md` | Common issues, how-tos |
+
+---
+
+## 🔗 External Resources
+
+- **Repository**: https://github.com/miams/rmagent
+- **RootsMagic**: https://www.rootsmagic.com/
+- **SQLite**: https://www.sqlite.org/docs.html
+- **LangChain**: https://python.langchain.com/
+
+---
+
+**Need help?** Check [faq.md](faq.md) or open an issue on GitHub.
diff --git a/docs/README.md b/docs/README.md
deleted file mode 100644
index 4997f9e..0000000
--- a/docs/README.md
+++ /dev/null
@@ -1,224 +0,0 @@
-# RMAgent Documentation Index
-
-Comprehensive documentation for RMAgent - AI-powered genealogy assistant for RootsMagic 11 databases.
-
-## 📚 Documentation Overview
-
-### For New Users
-
-Start here if you're new to RMAgent:
-
-1. **[README.md](../README.md)** - Project overview and quick start
-2. **[INSTALL.md](../INSTALL.md)** - Installation guide (all platforms)
-3. **[CONFIGURATION.md](../CONFIGURATION.md)** - Configuration and setup
-4. **[USAGE.md](../USAGE.md)** - Complete CLI command reference
-5. **[FAQ.md](../FAQ.md)** - Common questions and troubleshooting
-
-### For Developers
-
-Start here if you want to contribute or extend RMAgent:
-
-1. **[DEVELOPER_GUIDE.md](../DEVELOPER_GUIDE.md)** - Architecture, design patterns, API reference
-2. **[CONTRIBUTING.md](../CONTRIBUTING.md)** - Contribution workflow
-3. **[TESTING.md](../TESTING.md)** - Testing guide
-4. **[CHANGELOG.md](../CHANGELOG.md)** - Version history
-
-### Additional Documentation
-
-- **[USER_GUIDE.md](USER_GUIDE.md)** - Comprehensive user guide (31KB, all-in-one)
-- **[AGENTS.md](../AGENTS.md)** - Agent design patterns
-
----
-
-## 📖 Documentation by Topic
-
-### Installation & Setup
-
-| Document | Description | Audience |
-|----------|-------------|----------|
-| [INSTALL.md](../INSTALL.md) | Platform-specific installation (macOS, Linux, Windows/WSL2) | All users |
-| [CONFIGURATION.md](../CONFIGURATION.md) | Environment variables, LLM providers, prompt customization | All users |
-| [FAQ.md](../FAQ.md) | Troubleshooting installation issues | All users |
-
-### Using RMAgent
-
-| Document | Description | Audience |
-|----------|-------------|----------|
-| [USAGE.md](../USAGE.md) | All 7 CLI commands with 50+ examples | All users |
-| [USER_GUIDE.md](USER_GUIDE.md) | Comprehensive guide (installation → advanced usage) | All users |
-| [FAQ.md](../FAQ.md) | Common workflows and troubleshooting | All users |
-
-### Development
-
-| Document | Description | Audience |
-|----------|-------------|----------|
-| [DEVELOPER_GUIDE.md](../DEVELOPER_GUIDE.md) | Architecture, API reference, adding features | Developers |
-| [CONTRIBUTING.md](../CONTRIBUTING.md) | Git workflow, coding standards, PR process | Contributors |
-| [TESTING.md](../TESTING.md) | Test suite guide (279 tests, coverage analysis) | Developers |
-| [CHANGELOG.md](../CHANGELOG.md) | Complete version history | All |
-
-### Technical Reference
-
-| Document | Description | Audience |
-|----------|-------------|----------|
-| [AGENTS.md](../AGENTS.md) | Agent design patterns | Developers |
-| [data_reference/](../data_reference/) | RootsMagic 11 schema (18 docs) | Developers |
-
----
-
-## 🎯 Quick Navigation
-
-### By Task
-
-**I want to...**
-
-- **Install RMAgent** → [INSTALL.md](../INSTALL.md)
-- **Configure API keys** → [CONFIGURATION.md](../CONFIGURATION.md) (LLM Provider Setup)
-- **Generate a biography** → [USAGE.md](../USAGE.md) (Biography Command)
-- **Customize prompts** → [CONFIGURATION.md](../CONFIGURATION.md) (Prompt Customization)
-- **Run quality checks** → [USAGE.md](../USAGE.md) (Quality Command)
-- **Export to Hugo** → [USAGE.md](../USAGE.md) (Export Command)
-- **Fix errors** → [FAQ.md](../FAQ.md) (Troubleshooting)
-- **Add a new feature** → [DEVELOPER_GUIDE.md](../DEVELOPER_GUIDE.md) (Adding New Features)
-- **Run tests** → [TESTING.md](../TESTING.md) (Running Tests)
-- **Contribute code** → [CONTRIBUTING.md](../CONTRIBUTING.md) (Contribution Workflow)
-
-### By Role
-
-**New User:**
-1. [README.md](../README.md) → [INSTALL.md](../INSTALL.md) → [CONFIGURATION.md](../CONFIGURATION.md) → [USAGE.md](../USAGE.md)
-
-**Contributor:**
-1. [README.md](../README.md) → [CONTRIBUTING.md](../CONTRIBUTING.md) → [TESTING.md](../TESTING.md)
-
-**Developer (adding features):**
-1. [DEVELOPER_GUIDE.md](../DEVELOPER_GUIDE.md) → [CONTRIBUTING.md](../CONTRIBUTING.md) → [TESTING.md](../TESTING.md)
-
----
-
-## 📦 Project Documentation Files
-
-### Top-Level Documentation (8 files)
-
-Located in project root:
-
-```
-RM11/
-├── README.md              # Project overview & quick start
-├── INSTALL.md             # Installation guide (515 lines)
-├── USAGE.md               # CLI command reference (800+ lines)
-├── CONFIGURATION.md       # Configuration guide (1,000+ lines)
-├── FAQ.md                 # Common questions (550+ lines)
-├── CONTRIBUTING.md        # Contribution guidelines (450+ lines)
-├── TESTING.md             # Testing guide (600+ lines)
-├── CHANGELOG.md           # Version history (350+ lines)
-├── DEVELOPER_GUIDE.md     # Developer guide (1,000+ lines)
-└── AGENTS.md              # Agent design patterns
-```
-
-**Total:** 5,865+ lines of documentation
-
-### docs/ Directory
-
-Project-specific documentation:
-
-```
-docs/
-├── README.md              # This file - documentation index
-├── USER_GUIDE.md          # Comprehensive user guide (1,424 lines)
-├── MVP_CHECKPOINT.md      # Milestone 2 verification
-├── PHASE_5_COMPLETION.md  # Testing & Quality report
-├── PHASE_6_COMPLETION.md  # Documentation & Polish report
-├── AI_AGENT_TODO.md       # Project roadmap
-├── Test_Coverage_Analysis.md
-├── INTEGRATION_TESTING_SUMMARY.md
-├── REAL_API_VERIFICATION.md
-└── OPTIMIZATION_SUMMARY.md
-```
-
-### data_reference/ Directory
-
-RootsMagic 11 schema documentation (18 files):
-
-```
-data_reference/
-├── RM11_Schema_Reference.md         # Complete schema
-├── RM11_Date_Format.md              # 24-char date encoding
-├── RM11_Place_Format.md             # Place hierarchy
-├── RM11_FactTypes.md                # Event types
-├── RM11_BLOB_*.md                   # XML BLOB specs (3 files)
-├── RM11_Biography_Best_Practices.md # 9-section structure
-├── RM11_Data_Quality_Rules.md       # 24 validation rules
-├── RM11_Query_Patterns.md           # SQL patterns
-├── RM11_Timeline_Construction.md    # TimelineJS3 format
-└── ... (10 more reference docs)
-```
-
----
-
-## 🔍 Documentation Statistics
-
-**Total Documentation:**
-- **Lines:** 7,289+ lines
-- **Files:** 36 files (10 top-level + 10 docs/ + 16 data_reference/)
-- **Coverage:** Installation, usage, configuration, development, schema, API
-
-**By Category:**
-- **User Documentation:** 3,500+ lines (INSTALL, USAGE, CONFIGURATION, FAQ, USER_GUIDE)
-- **Developer Documentation:** 2,050+ lines (DEVELOPER_GUIDE, CONTRIBUTING, TESTING)
-- **Project Documentation:** 1,200+ lines (CHANGELOG, completion reports, roadmap)
-- **Schema Reference:** 18 files (data_reference/)
-
----
-
-## 📝 Documentation Updates
-
-### Recent Updates (v0.2.0 - October 12, 2025)
-
-**New Documentation:**
-- ✅ **DEVELOPER_GUIDE.md** - Comprehensive developer guide with architecture, API reference, adding features
-- ✅ **Prompt Customization** - Complete section in CONFIGURATION.md with YAML examples
-- ✅ **USER_GUIDE.md** - Updated to v0.2.0 with new prompt system
-
-**Updated Documentation:**
-- ✅ USER_GUIDE.md - "Customizing Prompts" section updated for YAML system
-- ✅ CONFIGURATION.md - Added 350+ line "Prompt Customization" section
-- ✅ CHANGELOG.md - Phase 5 and Phase 6 entries
-
-### Version History
-
-- **v0.2.0** (2025-10-12): Phase 5 & 6 complete - Testing, Quality, Documentation
-- **v0.1.0** (2025-10-10): MVP complete - All 8 CLI commands working
-- **v0.0.3** (2025-10-09): Milestone 1 - Working prototype
-
----
-
-## 🤝 Contributing to Documentation
-
-Documentation improvements are always welcome!
-
-**To contribute documentation:**
-
-1. **Small fixes:** Edit directly and submit PR
-2. **New sections:** Open issue first to discuss
-3. **Style guide:** Follow existing format
-4. **Examples:** Include practical code examples
-5. **Testing:** Verify all commands work
-
-See [CONTRIBUTING.md](../CONTRIBUTING.md) for details.
-
----
-
-## 📞 Getting Help
-
-**Questions about documentation:**
-- Open an issue: https://github.com/miams/rmagent/issues
-- Discussions: https://github.com/miams/rmagent/discussions
-
-**Found a bug in documentation:**
-- Report it: https://github.com/miams/rmagent/issues
-- Include: Which file, what's wrong, suggested fix
-
----
-
-**Last Updated:** October 12, 2025
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diff --git a/docs/guides/claude-code-setup.md b/docs/guides/claude-code-setup.md
new file mode 100644
index 0000000..48f5d6a
--- /dev/null
+++ b/docs/guides/claude-code-setup.md
@@ -0,0 +1,438 @@
+# Claude Code Setup for RMAgent
+
+This guide documents the slash commands and hooks configured for the RMAgent project.
+
+## Slash Commands
+
+All slash commands are defined in `.claude/commands/`. RMAgent-specific commands use the `rm-` prefix.
+
+**Total Commands: 12** (6 RMAgent-specific, 3 development, 3 utility)
+
+### RMAgent Commands (AI & Data)
+
+Commands that interact with RootsMagic database and AI features:
+
+#### `/rm-bio <person_id> [length]`
+**Description:** Generate a biography for a person using AI
+
+**Options:**
+- `show-prompt: true` - Shows the AI prompt
+- `meta: true` - Shows token usage and timing
+
+**Usage:**
+```
+/rm-bio 1                    # Standard biography
+/rm-bio 1 short              # Short biography
+/rm-bio 1 comprehensive      # Comprehensive biography
+```
+
+**Output:** Markdown file in `reports/biographies/`
+
+---
+
+#### `/rm-ask "<question>"`
+**Description:** Ask natural language questions about genealogy data using AI
+
+**Options:**
+- `show-prompt: true` - Shows the AI prompt
+- `meta: true` - Shows token usage and timing
+
+**Usage:**
+```
+/rm-ask "Who are the ancestors of John Smith?"
+/rm-ask "Find everyone born in Baltimore"
+/rm-ask "Show family relationships for person 1"
+```
+
+**Output:** AI-generated answer with data from database
+
+---
+
+#### `/rm-person <person_id> [options]`
+**Description:** Query person details from RootsMagic database
+
+**Usage:**
+```
+/rm-person 1                    # Basic info
+/rm-person 1 --events           # Include all events
+/rm-person 1 --family           # Include family relationships
+/rm-person 1 --ancestors        # Include ancestors
+/rm-person 1 --descendants      # Include descendants
+```
+
+**Output:** Formatted person information with requested details
+
+---
+
+#### `/rm-search [--name "Name"] [--place "Place"] [--limit N]`
+**Description:** Search database by name or place
+
+**Usage:**
+```
+/rm-search --name "John Smith"
+/rm-search --place "Baltimore"
+/rm-search --name "Smith" --limit 10
+```
+
+**Output:** List of matching persons with IDs
+
+---
+
+#### `/rm-quality [category]`
+**Description:** Run data quality validation
+
+**Categories:**
+- `dates` - Date format and range issues
+- `names` - Missing or invalid names
+- `places` - Place format issues
+- `relationships` - Relationship inconsistencies
+- `sources` - Citation and source issues
+- `events` - Event data issues
+
+**Usage:**
+```
+/rm-quality                  # All checks
+/rm-quality dates            # Only date issues
+/rm-quality names            # Only name issues
+```
+
+**Output:** Formatted table of data quality issues
+
+---
+
+#### `/rm-timeline <person_id> [options]`
+**Description:** Generate timeline visualization
+
+**Usage:**
+```
+/rm-timeline 1                      # JSON format
+/rm-timeline 1 --format html        # HTML format
+/rm-timeline 1 --include-family     # Include family events
+/rm-timeline 1 --group-by-phase     # Group by life phases
+```
+
+**Output:** TimelineJS3 JSON or HTML file
+
+---
+
+### Development Commands
+
+Generic development and testing commands (no `rm-` prefix):
+
+#### `/test [filter]`
+**Description:** Run pytest tests with optional filters
+
+**Usage:**
+```
+/test                    # Run all tests
+/test unit               # Run unit tests only
+/test integration        # Run integration tests only
+/test test_queries.py    # Run specific test file
+```
+
+**Output:** Test results with pass/fail status
+
+---
+
+#### `/coverage`
+**Description:** Run tests with coverage analysis
+
+**Usage:**
+```
+/coverage
+```
+
+**Output:** Coverage report with line-by-line analysis. HTML report at `htmlcov/index.html`
+
+---
+
+#### `/lint [fix]`
+**Description:** Run code quality checks (ruff + black)
+
+**Usage:**
+```
+/lint           # Check only
+/lint fix       # Auto-fix issues
+```
+
+**Output:** Linting errors and warnings
+
+---
+
+### Utility Commands
+
+#### `/docs [topic]`
+**Description:** Quick access to documentation
+
+**Usage:**
+```
+/docs                # Show INDEX.md
+/docs schema         # Schema reference
+/docs data-formats   # Data formats reference
+/docs dev            # Developer guide
+```
+
+**Output:** Documentation preview (first 50-80 lines)
+
+---
+
+#### `/doc-review [mode]`
+**Description:** Review documentation for accuracy and completeness using AI
+
+**Options:**
+- `show-prompt: true` - Shows the AI prompt
+- `meta: true` - Shows token usage and timing
+
+**Usage:**
+```
+/doc-review          # Brief mode: review root docs + INDEX.md
+/doc-review brief    # Same as above
+/doc-review deep     # Deep mode: review ALL documentation files
+```
+
+**Brief Mode Reviews:**
+- CLAUDE.md, README.md, AGENTS.md, CONTRIBUTING.md, CHANGELOG.md
+- docs/INDEX.md
+- Verifies INDEX.md accurately references all docs
+
+**Deep Mode Reviews:**
+- All files from brief mode
+- All documentation in docs/ directory
+- Cross-references and consistency checks
+
+**Output:** AI assessment with critical issues, recommendations, and specific fixes
+
+---
+
+#### `/check-db`
+**Description:** Verify database file exists and is accessible
+
+**Usage:**
+```
+/check-db
+```
+
+**Output:** Database path, status, and basic statistics (person/event/source counts)
+
+---
+
+## Claude Code Hooks
+
+Hooks are configured in `.claude/settings.local.json` and run automatically at specific events.
+
+### PostToolUse Hooks
+
+#### Coverage Reminder Hook
+**Trigger:** After running pytest with coverage (`uv run pytest --cov`)
+
+**Action:** Extracts coverage percentage and reminds to update CLAUDE.md and README.md if significantly changed
+
+**Output:**
+```
+📊 Test coverage: 88%
+💡 Reminder: Update coverage stats in CLAUDE.md and README.md if significantly changed
+```
+
+---
+
+### PreToolUse Hooks
+
+#### Git Push Confirmation Hook
+**Trigger:** Before git push commands
+
+**Action:** Shows recent commits being pushed
+
+**Output:**
+```
+⚠️  Pushing to remote. Recent commits:
+66a29ca docs: reorganize documentation structure
+4cdea76 fix: constrain caption width to match image margins
+528f1ef fix: handle sqlite3.Row objects in biography rendering
+```
+
+---
+
+## Git Pre-Commit Hook
+
+A standard git pre-commit hook is configured at `.git/hooks/pre-commit` to remind about documentation updates.
+
+**Triggers:**
+- Documentation structure changes → Check CLAUDE.md
+- Test modifications → Check README.md for coverage stats
+- Core code changes → Check CLAUDE.md
+- Dependency changes → Check README.md
+
+**Output:**
+```
+━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+⚠️  DOCUMENTATION REVIEW REMINDER
+━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+
+This commit may require updates to key documentation files:
+
+  • Documentation structure changed
+
+Please review and update if necessary:
+
+  ✓ CLAUDE.md     - Already modified
+  📄 README.md     - User-facing docs, badges, quick start
+  📄 AGENTS.md     - LangChain patterns, agent architecture
+
+Continue with commit? (y/n)
+```
+
+---
+
+## Configuration Files
+
+### `.claude/settings.local.json`
+- **Permissions:** Pre-approved bash commands, web fetch domains
+- **Hooks:** PostToolUse and PreToolUse hook configurations
+
+### `.claude/commands/`
+- All custom slash command definitions
+- Markdown files with frontmatter and bash scripts
+
+### `.git/hooks/pre-commit`
+- Git pre-commit hook for documentation review
+- Executable shell script
+
+---
+
+## Best Practices
+
+### When to Use Each Command
+
+**For Genealogy Work:**
+- Use `/rm-person` to quickly explore individuals
+- Use `/rm-search` to find people by name/place
+- Use `/rm-bio` when you need a formatted biography
+- Use `/rm-ask` for complex queries that need AI interpretation
+- Use `/rm-quality` regularly to maintain data integrity
+
+**For Development:**
+- Use `/test` for quick test runs during development
+- Use `/coverage` before committing to check test coverage
+- Use `/lint` before committing to catch style issues
+- Use `/check-db` when debugging database connection issues
+
+**For Documentation:**
+- Use `/docs` to quickly reference schema or data formats
+- Use `/doc-review` regularly to ensure docs stay accurate and current
+- Use `/doc-review brief` before major commits or PRs
+- Use `/doc-review deep` after significant feature additions
+- Keep CLAUDE.md, README.md, and AGENTS.md updated (hooks will remind you)
+
+### show-prompt and meta Flags
+
+Only use `show-prompt` and `meta` in commands that interact with LLMs:
+- ✅ `/rm-bio` - Generates biography with AI
+- ✅ `/rm-ask` - Uses AI to answer questions
+- ✅ `/doc-review` - Uses AI to review documentation
+- ❌ `/rm-person` - Pure database query
+- ❌ `/rm-search` - Pure database query
+- ❌ `/rm-quality` - Rule-based validation
+- ❌ `/rm-timeline` - Data extraction and formatting
+
+### Naming Conventions
+
+- **RMAgent-specific commands:** Use `rm-` prefix (`/rm-bio`, `/rm-person`)
+- **Generic dev commands:** No prefix (`/test`, `/lint`, `/coverage`)
+- **Utility commands:** No prefix (`/docs`, `/check-db`)
+
+---
+
+## Testing Your Setup
+
+After configuring slash commands and hooks:
+
+1. **Test a slash command:**
+   ```
+   /check-db
+   ```
+
+2. **Test an AI command:**
+   ```
+   /doc-review brief
+   ```
+
+3. **Test a hook:** Run pytest with coverage to see PostToolUse hook:
+   ```bash
+   uv run pytest --cov=rmagent
+   ```
+
+4. **Test git hook:** Make a change to tests and try to commit:
+   ```bash
+   # Modify a test file
+   git add tests/
+   git commit -m "test: update test"
+   # You should see the documentation review reminder
+   ```
+
+5. **View all commands:**
+   ```
+   /help
+   ```
+
+---
+
+## Troubleshooting
+
+### Slash commands not appearing
+- Check that files exist in `.claude/commands/`
+- Ensure markdown files have proper frontmatter
+- Restart Claude Code
+
+### Hooks not firing
+- Verify JSON syntax in `.claude/settings.local.json`
+- Check that regex matchers are properly escaped
+- Use `claude --debug` for detailed hook execution info
+
+### Git hook not running
+- Verify `.git/hooks/pre-commit` exists and is executable:
+  ```bash
+  chmod +x .git/hooks/pre-commit
+  ```
+- Check that it's not being bypassed with `--no-verify`
+
+---
+
+## Extending This Setup
+
+### Adding New Slash Commands
+
+1. Create `.claude/commands/your-command.md`:
+   ```markdown
+   ---
+   description: Your command description
+   show-prompt: true  # Only if uses AI
+   meta: true         # Only if uses AI
+   ---
+
+   Usage instructions here.
+
+   ```bash
+   # Your bash script
+   echo "Command output"
+   ```
+   ```
+
+2. Use `rm-` prefix if RMAgent-specific
+3. Document in this file
+
+### Adding New Hooks
+
+1. Edit `.claude/settings.local.json`
+2. Add to appropriate hook type (PreToolUse, PostToolUse, etc.)
+3. Use regex matcher to target specific tools
+4. Test thoroughly before committing
+
+---
+
+## References
+
+- **Claude Code Docs:** https://docs.claude.com/en/docs/claude-code/
+- **Slash Commands:** https://docs.claude.com/en/docs/claude-code/slash-commands
+- **Hooks:** https://docs.claude.com/en/docs/claude-code/hooks
+- **RMAgent User Guide:** [guides/user-guide.md](user-guide.md)
+- **Developer Guide:** [guides/developer-guide.md](developer-guide.md)
diff --git a/DEVELOPER_GUIDE.md b/docs/guides/developer-guide.md
similarity index 100%
rename from DEVELOPER_GUIDE.md
rename to docs/guides/developer-guide.md
diff --git a/docs/GIT_WORKFLOW_GUIDE.md b/docs/guides/git-workflow.md
similarity index 65%
rename from docs/GIT_WORKFLOW_GUIDE.md
rename to docs/guides/git-workflow.md
index 0d52c68..bd76ec8 100644
--- a/docs/GIT_WORKFLOW_GUIDE.md
+++ b/docs/guides/git-workflow.md
@@ -20,9 +20,22 @@ feature/*         Individual features
 
 ### Branches Explained
 
-- **main**: Production-ready code only. Protected - no direct commits allowed.
-- **develop**: Default working branch. All features merge here first.
+- **main**: Production-ready code only. **Protected** - no direct commits allowed.
+  - Requires PR with 1 approving review
+  - Requires all status checks to pass (linting + tests)
+  - Requires branch to be up-to-date before merge
+  - No force pushes or deletions allowed
+  - Enforced for administrators
+
+- **develop**: Default working branch. **Protected** - all features merge here first.
+  - Requires PR (self-merge allowed for solo dev)
+  - Requires all status checks to pass (linting + tests)
+  - No force pushes or deletions allowed
+  - Admins can bypass in emergencies
+
 - **feature/**: Individual features. Branch from develop, PR back to develop.
+  - No protection - you can commit directly and force push if needed
+  - Still requires PR to merge into develop
 
 ## Daily Workflow
 
@@ -75,6 +88,26 @@ git push
 - `refactor:` - Code refactoring
 - `chore:` - Maintenance tasks
 
+**Pre-Commit Hook** (Automatic):
+
+When you commit, a pre-commit hook automatically checks if key documentation files need updating:
+
+```
+⚠️  DOCUMENTATION REVIEW REMINDER
+
+This commit may require updates to key documentation files:
+
+  • Documentation structure changed
+
+Please review and update if necessary:
+
+  📄 CLAUDE.md     - Project overview, structure, key patterns
+  📄 README.md     - User-facing docs, badges, quick start
+  ✓ AGENTS.md     - Already modified
+```
+
+The hook will ask you to confirm before proceeding. This ensures CLAUDE.md, README.md, and AGENTS.md stay current.
+
 ### 3. Creating a Pull Request
 
 When your feature is ready:
@@ -91,10 +124,12 @@ gh pr create --base develop --title "feat: add census extraction" --body "Descri
 Or create the PR through GitHub web interface.
 
 **PR Checklist**:
-- [ ] All tests pass locally (`uv run pytest`)
-- [ ] Code is formatted (`uv run black .`)
-- [ ] No linting errors (`uv run ruff check .`)
+- [ ] All tests pass locally (`uv run pytest` or `/test`)
+- [ ] Code is formatted (`uv run black .` or `/lint fix`)
+- [ ] No linting errors (`uv run ruff check .` or `/lint`)
 - [ ] Changes are documented (if needed)
+- [ ] Pre-commit hook reviewed (auto-runs on commit)
+- [ ] CLAUDE.md, README.md, AGENTS.md updated if needed
 
 ### 4. Merging Your PR
 
@@ -193,13 +228,71 @@ git commit --amend --no-edit
 git push --force
 ```
 
-## GitHub Actions CI/CD
+## Automated Checks & Hooks
+
+RMAgent has three layers of automated checks:
+
+### 1. Git Pre-Commit Hook (Local)
+
+**Location:** `.git/hooks/pre-commit`
+
+**Triggers when:**
+- Documentation structure changes → Reminds to check CLAUDE.md
+- Test modifications → Reminds to check README.md for coverage stats
+- Core code changes → Reminds to check CLAUDE.md
+- Dependency updates → Reminds to check README.md
+
+**What it does:**
+- Detects changes that might affect key documentation
+- Shows which docs need review (with checkmarks for already-modified files)
+- Prompts to confirm before allowing commit
+- Prevents accidental outdated documentation
+
+**Example:**
+```
+⚠️  DOCUMENTATION REVIEW REMINDER
+
+  • Tests modified (check if coverage stats need updating)
+
+Please review and update if necessary:
+
+  ✓ CLAUDE.md     - Already modified
+  📄 README.md     - User-facing docs, badges, quick start
+  📄 AGENTS.md     - LangChain patterns, agent architecture
+
+Continue with commit? (y/n)
+```
+
+### 2. Claude Code Hooks (Development)
+
+**Location:** `.claude/settings.local.json`
+
+**PostToolUse Hook** - After running pytest with coverage:
+```
+📊 Test coverage: 88%
+💡 Reminder: Update coverage stats in CLAUDE.md and README.md if significantly changed
+```
+
+**PreToolUse Hook** - Before git push:
+```
+⚠️  Pushing to remote. Recent commits:
+66a29ca docs: reorganize documentation structure
+e3937b5 feat: add Claude Code slash commands
+```
+
+**See [`docs/guides/claude-code-setup.md`](claude-code-setup.md) for full hook documentation.**
+
+### 3. GitHub Actions CI/CD (Remote)
+
+**Location:** `.github/workflows/pr-tests.yml`
 
 Every PR automatically runs:
 1. **Linting** - `ruff check` and `black --check`
 2. **Tests** - Full test suite with coverage
 3. **Coverage Check** - Must maintain 80%+ coverage
 
+**Required for merge** due to branch protection on `develop` and `main`.
+
 **If tests fail**:
 1. Check the Actions tab on GitHub for error details
 2. Fix the issues locally
@@ -307,6 +400,9 @@ uv run pytest -vv -s
 5. **Test before PR** - Don't rely on CI to catch basic issues
 6. **One feature per branch** - Don't mix unrelated changes
 7. **Delete merged branches** - Keep your branch list clean
+8. **Trust the hooks** - Pre-commit and Claude Code hooks help maintain quality
+9. **Update docs proactively** - Don't wait for the hook to remind you
+10. **Use slash commands** - `/test`, `/lint`, `/coverage` for quick checks
 
 ## Resources
 
diff --git a/TESTING.md b/docs/guides/testing-guide.md
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