┌─────────────────────────────────────────────────────────────────┐
│                  CLAUDEMEM v0.3.0 ARCHITECTURE                   │
├─────────────────────────────────────────────────────────────────┤
│                                                                  │
│  ┌───────────────────────────────────────────────────────────┐  │
│  │                 AST STRUCTURAL LAYER ⭐NEW                  │  │
│  │  Tree-sitter Parse → Symbol Graph → PageRank Ranking       │  │
│  │  map | symbol | callers | callees | context                │  │
│  └───────────────────────────────────────────────────────────┘  │
│                              ↓                                   │
│  ┌───────────────────────────────────────────────────────────┐  │
│  │                    SEARCH LAYER                             │  │
│  │  Query → Embed → Vector Search + BM25 → Ranked Results     │  │
│  └───────────────────────────────────────────────────────────┘  │
│                              ↓                                   │
│  ┌───────────────────────────────────────────────────────────┐  │
│  │                     INDEX LAYER                             │  │
│  │  AST Parse → Chunk → Embed → LanceDB + Symbol Graph        │  │
│  └───────────────────────────────────────────────────────────┘  │
│                                                                  │
└─────────────────────────────────────────────────────────────────┘

# For agentic use, always use --agent flag for clean output
claudemem --agent <command>

# Core commands for agents
claudemem --agent map [query]              # Get structural overview (repo map)
claudemem --agent symbol <name>            # Find symbol definition
claudemem --agent callers <name>           # What calls this symbol?
claudemem --agent callees <name>           # What does this symbol call?
claudemem --agent context <name>           # Full context (symbol + dependencies)
claudemem --agent search <query>           # Semantic search (clean output)
claudemem --agent search <query> --map     # Search + include repo map context

claudemem --version

# Get version number
VERSION=$(claudemem --version 2>/dev/null | grep -oE '[0-9]+\.[0-9]+\.[0-9]+' | head -1)

# Check if v0.4.0+ features available
if [ -n "$VERSION" ] && printf '%s\n' "0.4.0" "$VERSION" | sort -V -C; then
  # v0.4.0+ available
  claudemem --agent dead-code  claudemem --agent test-gaps  claudemem --agent impact SymbolNameelse
  echo "Code analysis commands require claudemem v0.4.0+"
  echo "Current version: $VERSION"
  echo "Fallback to v0.3.0 commands (map, symbol, callers, callees)"
fi

# Try impact analysis (v0.4.0+), fallback to callers (v0.3.0)
IMPACT=$(claudemem --agent impact SymbolName  2>/dev/null)
if [ -n "$IMPACT" ] && [ "$IMPACT" != "command not found" ]; then
  echo "$IMPACT"
else
  echo "Using fallback (direct callers only):"
  claudemem --agent callers SymbolNamefi

# For a specific task, get focused repo map
claudemem --agent map "authentication flow"
# Output shows relevant symbols ranked by importance (PageRank):
# file: src/auth/AuthService.ts
# line: 15-89
# kind: class
# name: AuthService
# pagerank: 0.0921
# signature: class AuthService
# ---
# file: src/middleware/auth.ts
# ...

# Find exact location of a symbol
claudemem --agent symbol AuthService
# Output:
# file: src/auth/AuthService.ts
# line: 15-89
# kind: class
# name: AuthService
# signature: class AuthService implements IAuthProvider
# exported: true
# pagerank: 0.0921
# docstring: Handles user authentication and session management

# What calls AuthService? (impact of changes)
claudemem --agent callers AuthService
# Output:
# caller: LoginController.authenticate
# file: src/controllers/login.ts
# line: 34
# kind: call
# ---
# caller: SessionMiddleware.validate
# file: src/middleware/session.ts
# line: 12
# kind: call

# What does AuthService call? (its dependencies)
claudemem --agent callees AuthService
# Output:
# callee: Database.query
# file: src/db/database.ts
# line: 45
# kind: call
# ---
# callee: TokenManager.generate
# file: src/auth/tokens.ts
# line: 23
# kind: call

claudemem --agent context AuthService
# Output includes:
# [symbol]
# file: src/auth/AuthService.ts
# line: 15-89
# kind: class
# name: AuthService
# ...
# [callers]
# caller: LoginController.authenticate
# ...
# [callees]
# callee: Database.query
# ...

# Semantic search
claudemem --agent search "password hashing"
# Search with repo map context (recommended for complex tasks)
claudemem --agent search "password hashing" --map```

---

## Output Format

When using `--agent` flag, commands output machine-readable format:

Records are separated by `---`. Each field is `key: value` on its own line.

---

## Command Reference

### claudemem map [query]

Get structural overview of the codebase. Optionally focused on a query.

```bash
# Full repo map (top symbols by PageRank)
claudemem --agent map
# Focused on specific task
claudemem --agent map "authentication"
# Limit tokens
claudemem --agent map "auth" --tokens 500```

**Output fields**: file, line, kind, name, signature, pagerank, exported

**When to use**: Always first - understand structure before reading code

### claudemem symbol <name>

Find a symbol by name. Disambiguates using PageRank and export status.

```bash
claudemem --agent symbol Indexerclaudemem --agent symbol "search" --file retriever   # hint which file

claudemem --agent callers AuthService```

**Output fields**: caller (name), file, line, kind (call/import/extends/etc)

**When to use**: Before modifying anything - know the impact radius

### claudemem callees <name>

Find all symbols that the given symbol calls/references.

```bash
claudemem --agent callees AuthService```

**Output fields**: callee (name), file, line, kind

**When to use**: To understand dependencies and trace data flow

### claudemem context <name>

Get full context: the symbol plus its callers and callees.

```bash
claudemem --agent context Indexerclaudemem --agent context Indexer --callers 10 --callees 20```

**Output sections**: [symbol], [callers], [callees]

**When to use**: For complex modifications requiring full awareness

### claudemem search <query>

Semantic search across the codebase.

```bash
claudemem --agent search "error handling"claudemem --agent search "error handling" --map   # include repo map
claudemem --agent search "auth" -n 5   # limit results

# Find all unused symbols
claudemem --agent dead-code
# Stricter threshold (only very low PageRank)
claudemem --agent dead-code --max-pagerank 0.005
# Include exported symbols (usually excluded)
claudemem --agent dead-code --include-exported```

**Algorithm:**
- Zero callers (nothing references the symbol)
- Low PageRank (< 0.001 default)
- Not exported (by default, exports may be used externally)

**Output fields**: file, line, kind, name, pagerank, last_caller_removed

**When to use**: Architecture cleanup, tech debt assessment, before major refactoring

**Empty Result Handling:**
```bash
RESULT=$(claudemem --agent dead-code )
if [ -z "$RESULT" ] || [ "$RESULT" = "No dead code found" ]; then
  echo "Codebase is clean - no dead code detected!"
  echo "This indicates good code hygiene."
else
  echo "$RESULT"
fi

# Find all test coverage gaps
claudemem --agent test-gaps
# Only critical gaps (high PageRank)
claudemem --agent test-gaps --min-pagerank 0.05```

**Algorithm:**
- High PageRank (> 0.01 default) - Important code
- Zero callers from test files (*.test.ts, *.spec.ts, *_test.go)

**Output fields**: file, line, kind, name, pagerank, production_callers, test_callers

**When to use**: Test coverage analysis, QA planning, identifying critical gaps

**Empty Result Handling:**
```bash
RESULT=$(claudemem --agent test-gaps )
if [ -z "$RESULT" ] || [ "$RESULT" = "No test gaps found" ]; then
  echo "Excellent! All high-importance code has test coverage."
  echo "Consider lowering --min-pagerank threshold for additional coverage."
else
  echo "$RESULT"
fi

# Get all transitive callers
claudemem --agent impact UserService
# Limit depth for large codebases
claudemem --agent impact UserService --max-depth 5```

**Algorithm:**
- BFS traversal from symbol to all transitive callers
- Groups results by depth level
- Shows file:line for each caller

**Output sections**: direct_callers, transitive_callers (with depth), grouped_by_file

**When to use**: Before ANY modification, refactoring planning, risk assessment

**Empty Result Handling:**
```bash
RESULT=$(claudemem --agent impact FunctionName )
if [ -z "$RESULT" ] || echo "$RESULT" | grep -q "No callers found"; then
  echo "No callers found - this symbol appears unused or is an entry point."
  echo "If unused, consider running: claudemem --agent dead-code "
  echo "If entry point (API handler, main), this is expected."
else
  echo "$RESULT"
fi

# Navigation-focused search (prioritizes summaries)
claudemem --agent search "authentication" --use-case navigation
# Default search (balanced)
claudemem --agent search "authentication"```

**Navigation mode search weights:**
- `symbol_summary`: 1.5x (higher priority)
- `file_summary`: 1.3x (higher priority)
- `code_chunk`: 1.0x (normal)
- `idiom`: 1.2x (higher for pattern discovery)

### Symbol Summary Fields

```yaml
symbol: AuthService.authenticate
file: src/services/auth.ts
line: 45-89
behavior: "Validates user credentials and generates JWT token"
params:
  - name: credentials
    type: LoginCredentials
    description: "Email and password from login form"
returns:
  type: AuthResult
  description: "JWT token and user profile on success, error on failure"
side_effects:
  - "Updates user.lastLogin timestamp"
  - "Logs authentication attempt"
  - "May trigger rate limiting"

file: src/services/auth.ts
purpose: "Core authentication service handling login, logout, and session management"
exports:
  - AuthService (class)
  - authenticate (function)
  - validateToken (function)
patterns:
  - "Dependency Injection (constructor takes IUserRepository)"
  - "Factory Pattern (createSession)"
  - "Strategy Pattern (IAuthProvider interface)"
dependencies:
  - bcrypt (password hashing)
  - jsonwebtoken (JWT generation)
  - UserRepository (user data access)

# Find function behavior without reading code
claudemem --agent search "processPayment behavior" --use-case navigation
# Output includes symbol_summary:
# symbol: PaymentService.processPayment
# behavior: "Charges customer card via Stripe and saves transaction"
# side_effects: ["Updates balance", "Sends receipt email", "Logs to audit"]

# Find file purposes for architecture understanding
claudemem --agent search "file:services purpose" --use-case navigation
# Find anti-patterns to avoid
claudemem --agent search "anti_pattern SQL"```

### Regenerating Enrichments

If codebase changes significantly:

```bash
# Re-index with LLM enrichment
claudemem index --enrich

# Or enrich specific files
claudemem enrich src/services/payment.ts

# Step 1: Locate the symptom
SYMBOL=$(claudemem --agent symbol FunctionFromStackTrace )
if [ -z "$SYMBOL" ]; then
  echo "Symbol not found - check spelling or run: claudemem --agent map 'related keywords' "
  exit 1
fi

# Step 2: Get full context (callers + callees)
claudemem --agent context FunctionFromStackTrace
# Step 3: Trace backwards to find root cause
claudemem --agent callers suspectedSource
# Step 4: Check full impact of the bug (v0.4.0+)
IMPACT=$(claudemem --agent impact BuggyFunction  2>/dev/null)
if [ -n "$IMPACT" ]; then
  echo "$IMPACT"
else
  echo "Impact analysis requires claudemem v0.4.0+ or no callers found"
  echo "Fallback: claudemem --agent callers BuggyFunction "
fi

# Step 5: Read identified file:line ranges
# Fix bug, verify callers still work

# Step 6: Document impacted code for testing

## Bug Investigation Report

**Symptom:** [Description]
**Root Cause:** [Location and explanation]
**Call Chain:** [How we got here]
**Impact Radius:** [What else is affected]
**Fix Applied:** [What was changed]
**Verification:** [Tests run, callers checked]

# Step 1: Map the feature area
MAP=$(claudemem --agent map "feature area keywords" )
if [ -z "$MAP" ]; then
  echo "No matches found - try broader keywords"
fi

# Step 2: Identify extension points
claudemem --agent callees ExistingFeature
# Step 3: Get full context for modification point
claudemem --agent context ModificationPoint
# Step 4: Check existing patterns to follow
claudemem --agent search "similar pattern" --use-case navigation
# Step 5: Implement following existing patterns

# Step 6: Check test coverage gaps (v0.4.0+)
GAPS=$(claudemem --agent test-gaps  2>/dev/null)
if [ -n "$GAPS" ]; then
  echo "Test gaps to address:"
  echo "$GAPS"
else
  echo "test-gaps requires v0.4.0+ or no gaps found"
fi

## Feature Implementation Plan

**Feature:** [Description]
**Extension Point:** [Where to add]
**Dependencies:** [What it needs]
**Pattern to Follow:** [Existing similar code]
**Test Requirements:** [Coverage needs]

# Step 1: Find the symbol to refactor
SYMBOL=$(claudemem --agent symbol SymbolToRename )
if [ -z "$SYMBOL" ]; then
  echo "Symbol not found - check exact name"
  exit 1
fi

# Step 2: Get FULL impact (all transitive callers) (v0.4.0+)
IMPACT=$(claudemem --agent impact SymbolToRename  2>/dev/null)
if [ -n "$IMPACT" ]; then
  echo "$IMPACT"
  # (impact output includes grouped_by_file)
else
  echo "Using fallback (direct callers only):"
  claudemem --agent callers SymbolToRenamefi

# Step 3: Group by file for systematic updates

# Step 4: Update each caller location systematically

# Step 5: Verify all callers updated
claudemem --agent callers NewSymbolName
# Step 6: Run affected tests

## Refactoring Report

**Original:** [Old name/location]
**Target:** [New name/location]
**Direct Callers:** [Count]
**Transitive Callers:** [Count]
**Files Modified:** [List]
**Verification:** [All callers updated, tests pass]

# Step 1: Get full structural map
MAP=$(claudemem --agent map )
if [ -z "$MAP" ]; then
  echo "Index may be empty - run: claudemem index"
  exit 1
fi
echo "$MAP"

# Step 2: Identify architectural pillars (PageRank > 0.05)
# Document top 5 by PageRank

# Step 3: For each pillar, get full context
claudemem --agent context PillarSymbol
# Step 4: Trace major flows via callees
claudemem --agent callees EntryPoint
# Step 5: Identify dead code (cleanup opportunities) (v0.4.0+)
DEAD=$(claudemem --agent dead-code  2>/dev/null)
if [ -n "$DEAD" ]; then
  echo "Dead code found:"
  echo "$DEAD"
else
  echo "No dead code found (or v0.4.0+ required)"
fi

# Step 6: Identify test gaps (risk areas) (v0.4.0+)
GAPS=$(claudemem --agent test-gaps  2>/dev/null)
if [ -n "$GAPS" ]; then
  echo "Test gaps:"
  echo "$GAPS"
else
  echo "No test gaps found (or v0.4.0+ required)"
fi

## Architecture Report

**Core Abstractions (PageRank > 0.05):**
1. [Symbol] - [Role in system]
2. [Symbol] - [Role in system]
3. [Symbol] - [Role in system]

**Layer Structure:**

**Major Flows:**
- [Flow 1: Entry -> Processing -> Output]
- [Flow 2: Entry -> Processing -> Output]

**Health Indicators:**
- Dead Code: [Count] symbols
- Test Gaps: [Count] high-importance untested
- Tech Debt: [Summary]

# Step 1: Map security-related code
claudemem --agent map "auth permission security token"
# Step 2: Find authentication entry points
SYMBOL=$(claudemem --agent symbol authenticate )
if [ -z "$SYMBOL" ]; then
  echo "No 'authenticate' symbol - try: login, verify, validate"
fi
claudemem --agent callers authenticate
# Step 3: Trace authentication flow
claudemem --agent callees authenticate
# Step 4: Check authorization patterns
claudemem --agent map "authorize permission check guard"
# Step 5: Find sensitive data handlers
claudemem --agent map "password hash token secret key"
# Step 6: Check for test coverage on security code (v0.4.0+)
GAPS=$(claudemem --agent test-gaps --min-pagerank 0.01  2>/dev/null)
if [ -n "$GAPS" ]; then
  # Filter for security-related symbols
  echo "$GAPS" | grep -E "(auth|login|password|token|permission|secret)"
fi

## Security Audit Report

**Authentication:**
- Entry Points: [List]
- Flow: [Description]
- Gaps: [Issues found]

**Authorization:**
- Permission Checks: [Where implemented]
- Coverage: [All routes covered?]

**Sensitive Data:**
- Password Handling: [How stored/compared]
- Token Management: [Generation/validation]
- Secrets: [How managed]

**Test Coverage:**
- Security Code Coverage: [X%]
- Critical Gaps: [List]

**Recommendations:**
1. [Priority 1 fix]
2. [Priority 2 fix]

// NOT visible to static analysis
const module = await import(`./modules/${name}`);

// Exported for external use
export function publicAPI() { ... }

// NOT visible to static analysis
const fn = obj[methodName]();
eval("functionName()");

// NOT visible as direct callers
emitter.on('event', handler);
document.addEventListener('click', onClick);

// Container registration hides relationships
container.register(IService, ServiceImpl);

# Step 1: Get overview of auth-related code
claudemem --agent map "authentication null pointer"
# Step 2: Locate the specific symbol mentioned in error
claudemem --agent symbol authenticate
# Step 3: Check what calls it (to understand how it's used)
claudemem --agent callers authenticate
# Step 4: Read the actual code at the identified location
# Now you know exactly which file:line to read

# Step 1: Understand API structure
claudemem --agent map "API endpoints rate"
# Step 2: Find the main API handler
claudemem --agent symbol APIController
# Step 3: See what the API controller depends on
claudemem --agent callees APIController
# Step 4: Check if rate limiting already exists somewhere
claudemem --agent search "rate limit"
# Step 5: Get full context for the modification point
claudemem --agent context APIController```

### Scenario 3: Refactoring

**Task**: "Rename DatabaseConnection to DatabasePool"

```bash
# Step 1: Find the symbol
claudemem --agent symbol DatabaseConnection
# Step 2: Find ALL callers (these all need updating)
claudemem --agent callers DatabaseConnection
# Step 3: The output shows every file:line that references it
# Update each location systematically

# Step 1: Get high-level structure
claudemem --agent map "indexing pipeline"
# Step 2: Find the main entry point (highest PageRank)
claudemem --agent symbol Indexer
# Step 3: Trace the flow - what does Indexer call?
claudemem --agent callees Indexer
# Step 4: For each major callee, get its callees
claudemem --agent callees VectorStoreclaudemem --agent callees FileTracker
# Now you have the full pipeline traced

1. RECEIVE TASK
   ↓
2. claudemem --agent map "<task keywords>"   → Understand structure, identify key symbols
   ↓
3. claudemem --agent symbol <high-pagerank-symbol>   → Get exact location
   ↓
4. claudemem --agent callers <symbol>   (if modifying)
   → Know the impact radius
   ↓
5. claudemem --agent callees <symbol>   (if needed)
   → Understand dependencies
   ↓
6. READ specific file:line ranges (not whole files)
   ↓
7. MAKE CHANGES with full awareness
   ↓
8. CHECK callers still work

┌─────────────────────────────────────────────────────────────────┐
│                 CORRECT INVESTIGATION FLOW (v0.3.0)              │
├─────────────────────────────────────────────────────────────────┤
│                                                                  │
│  1. claudemem --agent map "task"                          │
│     → Understand structure, find high-PageRank symbols          │
│                                                                  │
│  2. claudemem --agent symbol <name>                       │
│     → Get exact file:line location                              │
│                                                                  │
│  3. claudemem --agent callers <name>                      │
│     → Know impact radius BEFORE modifying                       │
│                                                                  │
│  4. claudemem --agent callees <name>                      │
│     → Understand dependencies                                    │
│                                                                  │
│  5. Read specific file:line ranges (NOT whole files)            │
│                                                                  │
│  6. Make changes with full awareness                            │
│                                                                  │
│  ⚠️ NEVER: Start with Read/Glob for semantic questions          │
│  ⚠️ NEVER: Modify without checking callers                      │
│  ⚠️ NEVER: Search without mapping first                         │
│                                                                  │
└─────────────────────────────────────────────────────────────────┘

# Check if claudemem CLI is available
which claudemem || command -v claudemem

# Check version (must be 0.3.0+)
claudemem --version

# npm (recommended)
npm install -g claude-codemem

# Homebrew (macOS)
brew tap MadAppGang/claude-mem && brew install --cask claudemem

# Index current project
claudemem index

# Check status
claudemem --version && ls -la .claudemem/index.db 2>/dev/null

# Core documentation commands
claudemem docs status            # Show indexed libraries and cache state
claudemem docs fetch             # Fetch docs for all detected dependencies
claudemem docs fetch react vue   # Fetch specific libraries
claudemem docs providers         # List available documentation providers
claudemem docs refresh           # Force refresh all cached documentation
claudemem docs clear             # Clear all documentation cache
claudemem docs clear react       # Clear specific library cache

# Option 1: Run init (includes docs configuration)
claudemem init

# Option 2: Configure Context7 manually (optional, for best coverage)
export CONTEXT7_API_KEY=your_key

# Get free API key at: https://context7.com/dashboard

# Check current documentation status
claudemem docs status

# Output:
# 📚 Documentation Status
#
#   Enabled:     Yes
#   Providers:   Context7, llms.txt, DevDocs
#   Libraries:   12 indexed
#   Cache Age:   2h 15m
#
#   Indexed Libraries:
#     react (v18) via Context7 - 145 chunks
#     typescript (v5) via Context7 - 89 chunks
#     express (v4) via llms.txt - 34 chunks
#     ...

# Fetch documentation for all project dependencies
claudemem docs fetch

# Output:
# 📚 Fetching Documentation
#
#   [1/8] react... ✓ 145 chunks via Context7
#   [2/8] typescript... ✓ 89 chunks via Context7
#   [3/8] express... ✓ 34 chunks via llms.txt
#   [4/8] lodash... ✓ 67 chunks via DevDocs
#   ...

# Fetch specific library
claudemem docs fetch fastapi

# View available providers
claudemem docs providers

# Force refresh (clears cache, refetches)
claudemem docs refresh

claudemem --agent search "how to use React hooks"
# Output includes:
# --- Your Code ---
# file: src/components/UserProfile.tsx
# line: 12-45
# kind: function
# name: useUserProfile
# score: 0.89
# content: Custom hook for user profile management...
# ---
# --- React Documentation ---
# library: react
# section: Hooks Reference
# title: useEffect
# score: 0.87
# content: The useEffect Hook lets you perform side effects...
# ---
# library: react
# section: Hooks Reference
# title: useState
# score: 0.85
# content: useState is a Hook that lets you add state...

# ENHANCED Investigation Workflow (v0.7.0+)

# Step 0: Ensure framework docs are available (one-time)
claudemem docs status || claudemem docs fetch

# Step 1: Map architecture (now includes library patterns)
claudemem --agent map "authentication"
# Step 2: Search both code AND framework docs
claudemem --agent search "JWT token validation"# Returns: your auth code + library docs on JWT handling

# Step 3: Understand how the library recommends usage
claudemem --agent search "react best practices hooks"# Returns: your patterns + React official guidance

claudemem --version
# Expected: 0.7.0 or higher

# After using search results, report feedback
claudemem feedback --query "your original query" \
  --helpful id1,id2 \
  --unhelpful id3,id4

# Result IDs are shown in search output:
claudemem search "authentication" --agent# Output includes:
# id: abc123
# file: src/auth/middleware.ts
# ...

{
  "tool": "report_search_feedback",
  "arguments": {
    "query": "authentication flow",
    "allResultIds": ["id1", "id2", "id3"],
    "helpfulIds": ["id1"],
    "unhelpfulIds": ["id3"]
  }
}

# Template 1: Bug Investigation (add at end)
# Step 7: Report feedback
if [ -n "$SEARCH_QUERY" ] && [ -n "$HELPFUL_IDS" ]; then
  # Check if feedback is available (v0.8.0+)
  if claudemem feedback --help 2>&1 | grep -qi "feedback"; then
    timeout 5 claudemem feedback --query "$SEARCH_QUERY" \
      --helpful "${HELPFUL_IDS}" \
      --unhelpful "${UNHELPFUL_IDS}" 2>/dev/null || true
  else
    echo "Note: Search feedback requires claudemem v0.8.0+"
  fi
fi

# Full investigation with feedback tracking

# 0. Check if feedback is available (v0.8.0+)
FEEDBACK_AVAILABLE=false
if claudemem feedback --help 2>&1 | grep -qi "feedback"; then
  FEEDBACK_AVAILABLE=true
else
  echo "Note: Search feedback requires claudemem v0.8.0+"
fi

# 1. Search and capture IDs
RESULTS=$(claudemem --agent search "payment processing" -n 10 )
ALL_IDS=$(echo "$RESULTS" | grep "^id:" | awk '{print $2}')
SEARCH_QUERY="payment processing"

# 2. Initialize tracking arrays
HELPFUL=()
UNHELPFUL=()

# 3. Process results (during investigation)
# When you read a result and it's useful:
HELPFUL+=("abc123")
# When you read a result and it's not relevant:
UNHELPFUL+=("def456")

# 4. Report feedback (at end of investigation)
if [ "$FEEDBACK_AVAILABLE" = true ] && ([ ${#HELPFUL[@]} -gt 0 ] || [ ${#UNHELPFUL[@]} -gt 0 ]); then
  timeout 5 claudemem feedback \
    --query "$SEARCH_QUERY" \
    --helpful "$(IFS=,; echo "${HELPFUL[*]}")" \
    --unhelpful "$(IFS=,; echo "${UNHELPFUL[*]}")" \
    2>/dev/null || echo "Note: Feedback not sent (optional)"
fi

# Count files modified since last index
STALE_COUNT=$(find . -type f \( -name "*.ts" -o -name "*.tsx" -o -name "*.js" -o -name "*.jsx" -o -name "*.py" -o -name "*.go" -o -name "*.rs" \) \
  -newer .claudemem/index.db 2>/dev/null | grep -v "node_modules" | grep -v ".git" | grep -v "dist" | grep -v "build" | wc -l)
STALE_COUNT=$((STALE_COUNT + 0))  # Normalize to integer

if [ "$STALE_COUNT" -gt 0 ]; then
  # Get index time with explicit platform detection
  if [[ "$OSTYPE" == "darwin"* ]]; then
    INDEX_TIME=$(stat -f "%Sm" -t "%Y-%m-%d %H:%M" .claudemem/index.db 2>/dev/null)
  else
    INDEX_TIME=$(stat -c "%y" .claudemem/index.db 2>/dev/null | cut -d'.' -f1)
  fi
  INDEX_TIME=${INDEX_TIME:-"unknown time"}

  # Use AskUserQuestion to ask user how to proceed
  # Options: [1] Reindex now (Recommended), [2] Proceed with stale index, [3] Cancel
fi

AskUserQuestion({
  questions: [{
    question: `${STALE_COUNT} files have been modified since the last index (${INDEX_TIME}). The claudemem index may be outdated, which could cause missing or incorrect results. How would you like to proceed?`,
    header: "Index Freshness Warning",
    multiSelect: false,
    options: [
      {
        label: "Reindex now (Recommended)",
        description: "Run claudemem index to update. Takes ~1-2 minutes."
      },
      {
        label: "Proceed with stale index",
        description: "Continue investigation. May miss recent code changes."
      },
      {
        label: "Cancel investigation",
        description: "I'll handle this manually."
      }
    ]
  }]
})

# map validation
RESULTS=$(claudemem --agent map "authentication" )
EXIT_CODE=$?

if [ "$EXIT_CODE" -ne 0 ]; then
  echo "ERROR: claudemem command failed"
  # Diagnose index health
  DIAGNOSIS=$(claudemem --version && ls -la .claudemem/index.db 2>&1)
  # Use AskUserQuestion
fi

if [ -z "$RESULTS" ]; then
  echo "WARNING: No results found - may need reindex or different query"
  # Use AskUserQuestion
fi

if ! echo "$RESULTS" | grep -qi "auth\|login\|user\|session"; then
  echo "WARNING: Results may not be relevant to authentication query"
  # Use AskUserQuestion
fi

# symbol validation
RESULTS=$(claudemem --agent symbol UserService )
if ! echo "$RESULTS" | grep -q "name: UserService"; then
  echo "WARNING: UserService not found - check spelling or reindex"
  # Use AskUserQuestion
fi

# search validation
RESULTS=$(claudemem --agent search "error handling" )
MATCH_COUNT=0
for kw in error handling catch try; do
  if echo "$RESULTS" | grep -qi "$kw"; then
    MATCH_COUNT=$((MATCH_COUNT + 1))
  fi
done
if [ "$MATCH_COUNT" -lt 2 ]; then
  echo "WARNING: Results may not be relevant to error handling query"
  # Use AskUserQuestion
fi