refactor: remove MCP code-index dependency, replace with ripgrep/find

Replace all mcp__code-index__ calls with native ripgrep and find commands
across workflow and command files for better performance and portability.

Changes:
- Remove 41 mcp__code-index__ function calls from 12 files
- Replace with ripgrep (rg) for content search
- Replace with find for file discovery
- Remove index refresh dependencies (no longer needed)

Modified files:
- workflow/tools: context-gather, test-context-gather, task-generate-agent,
  task-generate, test-task-generate (core workflow tools)
- workflow: review (security scanning)
- memory: load, update-related, docs (memory management)
- cli/mode: plan, bug-index, code-analysis (CLI modes)

Documentation updates:
- Simplify mcp-tool-strategy.md to only Exa usage (5 lines)
- Streamline context-search-strategy.md to 69 lines
- Standardize codebase-retrieval syntax per intelligent-tools-strategy.md

Benefits:
- Faster search with ripgrep (no index overhead)
- Better cross-platform compatibility
- Simpler configuration (fewer MCP dependencies)
- -232 lines of code removed

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

.claude/commands/cli/mode/bug-index.md

@@ -138,7 +138,7 @@ RULES: $(cat ~/.claude/prompt-templates/bug-fix.md) | Bug: token validation fail
 ```bash
 # 1. Find bug-related files
 rg "error_keyword" --files-with-matches
-mcp__code-index__search_code_advanced(pattern="error|exception", file_pattern="*.ts")
+rg "error|exception" -g "*.ts"
 
 # 2. Execute bug analysis with focused context (analysis only, no code changes)
 /cli:mode:bug-index --cd "src/module" "specific error description"

.claude/commands/cli/mode/code-analysis.md

@@ -141,7 +141,7 @@ RULES: $(cat ~/.claude/prompt-templates/code-analysis.md) | Focus on security
 ```bash
 # 1. Find entry points and related files
 rg "function.*authenticate|class.*AuthService" --files-with-matches
-mcp__code-index__search_code_advanced(pattern="authenticate|login", file_pattern="*.ts")
+rg "authenticate|login" -g "*.ts"
 
 # 2. Build call graph understanding
 # entry → middleware → service → repository

.claude/commands/cli/mode/plan.md

@@ -139,7 +139,7 @@ RULES: $(cat ~/.claude/prompt-templates/plan.md) | Maintain backward compatibili
 ```bash
 # 1. Discover project structure
 ~/.claude/scripts/get_modules_by_depth.sh
-mcp__code-index__find_files(pattern="*.ts")
+find . -name "*.ts" -type f
 
 # 2. Gather existing architecture info
 rg "architecture|design" --files-with-matches

.claude/commands/memory/docs.md

@@ -658,7 +658,7 @@ bash(
     "pre_analysis": [
       {
         "step": "discover_api_endpoints",
-        "command": "mcp__code-index__search_code_advanced(pattern='router\\.|@(Get|Post)', file_pattern='*.{ts,js}')",
+        "command": "bash(rg 'router\\.| @(Get|Post)' -g '*.{ts,js}')",
         "output_to": "endpoint_discovery"
       },
       {

.claude/commands/memory/load.md

@@ -121,14 +121,14 @@ Task(
 ### Step 2: Keyword Extraction & File Discovery
 
 1. Extract core keywords from task description
-2. Discover relevant files using MCP code-index or rg:
-   \`\`\`javascript
-   // Prefer MCP tools
-   mcp__code-index__find_files(pattern="*{keyword}*")
-   mcp__code-index__search_code_advanced(pattern="{keyword}", context_lines=2)
+2. Discover relevant files using ripgrep and find:
+   \`\`\`bash
+   # Find files by name
+   find . -name "*{keyword}*" -type f
 
-   // Fallback: use rg
-   bash(rg -l "{keyword}" --type ts --type md)
+   # Search content with ripgrep
+   rg "{keyword}" --type ts --type md -C 2
+   rg -l "{keyword}" --type ts --type md  # List files only
    \`\`\`
 
 ### Step 3: Deep Analysis via CLI

.claude/commands/memory/update-related.md

@@ -40,10 +40,7 @@ Orchestrates context-aware CLAUDE.md updates for changed modules using batched a
 ## Phase 1: Change Detection & Analysis
 
 ```bash
-# Refresh code index
-bash(mcp__code-index__refresh_index)
-
-# Detect changed modules
+# Detect changed modules (no index refresh needed)
 bash(~/.claude/scripts/detect_changed_modules.sh list)
 
 # Cache git changes

.claude/commands/workflow/review.md

@@ -92,10 +92,10 @@ After bash validation, the model takes control to:
 2. **Perform Specialized Review**: Based on `review_type`
 
    **Security Review** (`--type=security`):
-   - Use MCP code search for security patterns:
+   - Use ripgrep for security patterns:
      ```bash
-     mcp__code-index__search_code_advanced(pattern="password|token|secret|auth", file_pattern="*.{ts,js,py}")
-     mcp__code-index__search_code_advanced(pattern="eval|exec|innerHTML|dangerouslySetInnerHTML", file_pattern="*.{ts,js,tsx}")
+     rg "password|token|secret|auth" -g "*.{ts,js,py}"
+     rg "eval|exec|innerHTML|dangerouslySetInnerHTML" -g "*.{ts,js,tsx}"
      ```
    - Use Gemini for security analysis:
      ```bash

.claude/commands/workflow/tools/context-gather.md

@@ -17,7 +17,7 @@ Agent-driven intelligent context collector that gathers relevant information fro
 - **Agent-Driven**: Delegate execution to universal-executor agent for autonomous operation
 - **Two-Phase Flow**: Discovery (context loading) → Execution (context gathering and packaging)
 - **Memory-First**: Reuse loaded documents from conversation memory
-- **MCP-Enhanced**: Use MCP tools for advanced code analysis and file discovery
+- **Ripgrep-Enhanced**: Use ripgrep and native tools for code analysis and file discovery
 - **Intelligent Collection**: Auto-identify relevant resources based on keyword analysis
 - **Comprehensive Coverage**: Collect code, documentation, configurations, and dependencies
 - **Standardized Output**: Generate unified format context-package.json
@@ -36,9 +36,10 @@ Agent-driven intelligent context collector that gathers relevant information fro
     // If in memory: use cached content
     // Else: Load from .workflow/{session-id}/workflow-session.json
   },
-  "mcp_capabilities": {
-    // Agent will use these tools to discover project context
-    "code_index": true,
+  "search_tools": {
+    // Agent will use these native tools to discover project context
+    "ripgrep": true,
+    "find": true,
     "exa_code": true,
     "exa_web": true
   }
@@ -76,8 +77,9 @@ Task(
 ### Session Metadata
 {session_metadata_content}
 
-### MCP Capabilities
-- code-index: Available for file discovery and code search
+### Search Tools
+- ripgrep: Available for content search and pattern matching
+- find: Available for file discovery
 - exa-code: Available for external research
 - exa-web: Available for web search
 
@@ -87,7 +89,7 @@ Task(
 1. **Project Structure Analysis**: Execute get_modules_by_depth.sh for architecture overview
 2. **Documentation Loading**: Load CLAUDE.md, README.md and relevant documentation
 3. **Keyword Extraction**: Extract core keywords from task description
-4. **Smart File Discovery**: Use MCP code-index tools to locate relevant files
+4. **Smart File Discovery**: Use ripgrep and find to locate relevant files
 5. **Code Structure Analysis**: Analyze project structure to identify relevant modules
 6. **Dependency Discovery**: Identify tech stack and dependency relationships
 7. **Context Packaging**: Generate standardized JSON context package
@@ -120,22 +122,18 @@ Task(
    - Identify potentially involved modules and components
    - Set file type filters
 
-#### Step 2: MCP-Enhanced File Discovery
+#### Step 2: File Discovery with Native Tools
 1. **Code File Location**
-   Use MCP code-index tools:
-   \`\`\`javascript
-   // Find files by pattern
-   mcp__code-index__find_files(pattern="*{keyword}*")
+   Use ripgrep and find commands:
+   \`\`\`bash
+   # Find files by pattern
+   find . -name "*{keyword}*" -type f
 
-   // Search code content
-   mcp__code-index__search_code_advanced(
-     pattern="{keyword_patterns}",
-     file_pattern="*.{ts,js,py,go,md}",
-     context_lines=3
-   )
+   # Search code content with ripgrep
+   rg "{keyword_patterns}" --type-add 'custom:*.{ts,js,py,go,md}' -t custom -C 3
 
-   // Get file summaries
-   mcp__code-index__get_file_summary(file_path="relevant/file.ts")
+   # Get file summaries (find function/class definitions)
+   rg "^(class|function|export|def|interface)" relevant/file.ts
    \`\`\`
 
 2. **Configuration Files Discovery**
@@ -321,34 +319,27 @@ Before completion, verify:
 - File count limit: Maximum 50 files per type
 - Size filtering: Skip oversized files (>10MB)
 - Depth limit: Maximum search depth of 3 levels
-- Use MCP tools for efficient discovery
+- Use ripgrep for efficient discovery
 
-**MCP Tools Integration**:
-Agent should use MCP code-index tools when available:
-\`\`\`javascript
-// Set project path
-mcp__code-index__set_project_path(path="{current_project_path}")
+**Native Tools Integration**:
+Agent should use ripgrep and find commands:
+\`\`\`bash
+# Find files by pattern
+find . -name "*{keyword}*" -type f
 
-// Refresh index
-mcp__code-index__refresh_index()
+# Search code content with ripgrep
+rg "{keyword_patterns}" --type ts --type js --type py --type go --type md -C 3
 
-// Find files by pattern
-mcp__code-index__find_files(pattern="*{keyword}*")
+# Alternative: use glob patterns
+rg "{keyword_patterns}" -g "*.{ts,js,py,go,md}" -C 3
 
-// Search code content
-mcp__code-index__search_code_advanced(
-  pattern="{keyword_patterns}",
-  file_pattern="*.{ts,js,py,go,md}",
-  context_lines=3
-)
+# Count matches
+rg "{keyword_patterns}" -c
+
+# List files with matches
+rg "{keyword_patterns}" --files-with-matches
 \`\`\`
 
-**Fallback Strategy**:
-When MCP tools unavailable, agent should use traditional commands:
-- \`find\` for file discovery
-- \`rg\` or \`grep\` for content search
-- Bash commands from project structure analysis
-
 ## Output
 
 Generate context-package.json and report completion:
@@ -391,9 +382,10 @@ const agentContext = {
     ? memory.get("workflow-session.json")
     : Read(.workflow/WFS-[id]/workflow-session.json),
 
-  // MCP capabilities - agent will use these tools
-  mcp_capabilities: {
-    code_index: true,
+  // Search tools - agent will use these native tools
+  search_tools: {
+    ripgrep: true,
+    find: true,
     exa_code: true,
     exa_web: true
   }

.claude/commands/workflow/tools/task-generate-agent.md

@@ -93,14 +93,11 @@ Autonomous task JSON and IMPL_PLAN.md generation using action-planning-agent wit
    }
    ```
 
-5. **MCP Code Analysis** (optional - enhance understanding)
-   ```javascript
-   // Find relevant files for task context
-   mcp__code-index__find_files(pattern="*auth*")
-   mcp__code-index__search_code_advanced(
-     pattern="authentication|oauth",
-     file_pattern="*.ts"
-   )
+5. **Code Analysis with Native Tools** (optional - enhance understanding)
+   ```bash
+   # Find relevant files for task context
+   find . -name "*auth*" -type f
+   rg "authentication|oauth" -g "*.ts"
    ```
 
 6. **MCP External Research** (optional - gather best practices)
@@ -274,18 +271,13 @@ $(cat ~/.claude/workflows/cli-templates/prompts/workflow/impl-plan-template.txt)
 **Code Index Usage**:
 \`\`\`javascript
 // Discover authentication-related files
-mcp__code-index__find_files(pattern="*auth*")
+bash(find . -name "*auth*" -type f)
 
 // Search for OAuth patterns
-mcp__code-index__search_code_advanced(
-  pattern="oauth|jwt|authentication",
-  file_pattern="*.{ts,js}"
-)
+bash(rg "oauth|jwt|authentication" -g "*.{ts,js}")
 
 // Get file summary for key components
-mcp__code-index__get_file_summary(
-  file_path="src/auth/index.ts"
-)
+bash(rg "^(class|function|export|interface)" src/auth/index.ts)
 \`\`\`
 
 **Exa Research Usage**:

.claude/commands/workflow/tools/task-generate.md

@@ -249,9 +249,9 @@ This enhanced 5-field schema embeds all necessary context, artifacts, and execut
         }
       },
       {
-        "step": "mcp_codebase_exploration",
-        "action": "Explore codebase using MCP tools",
-        "command": "mcp__code-index__find_files(pattern=\"[patterns]\") && mcp__code-index__search_code_advanced(pattern=\"[patterns]\")",
+        "step": "codebase_exploration",
+        "action": "Explore codebase using native tools",
+        "command": "bash(find . -name \"[patterns]\" -type f && rg \"[patterns]\")",
         "output_to": "codebase_structure"
       },
       {

.claude/commands/workflow/tools/test-context-gather.md

@@ -17,11 +17,11 @@ Specialized context collector for test generation workflows that analyzes test c
 - **Gap Identification**: Locate implementation files without corresponding tests
 - **Source Context Loading**: Import implementation summaries from source session
 - **Framework Detection**: Auto-detect test framework and patterns
-- **MCP-Powered**: Leverage code-index tools for precise analysis
+- **Ripgrep-Powered**: Leverage ripgrep and native tools for precise analysis
 
 ## Core Responsibilities
 - Load source session implementation context
-- Analyze current test coverage using MCP tools
+- Analyze current test coverage using ripgrep
 - Identify files requiring test generation
 - Detect test framework and conventions
 - Package test context for analysis phase
@@ -41,21 +41,17 @@ Specialized context collector for test generation workflows that analyzes test c
    - Extract changed files and implementation scope
    - Identify implementation patterns and tech stack
 
-### Phase 2: Test Coverage Analysis (MCP Tools)
+### Phase 2: Test Coverage Analysis (Ripgrep)
 
 1. **Existing Test Discovery**
    ```bash
    # Find all test files
-   mcp__code-index__find_files(pattern="*.test.*")
-   mcp__code-index__find_files(pattern="*.spec.*")
-   mcp__code-index__find_files(pattern="*test_*.py")
+   find . -name "*.test.*" -type f
+   find . -name "*.spec.*" -type f
+   find . -name "*test_*.py" -type f
 
    # Search for test patterns
-   mcp__code-index__search_code_advanced(
-     pattern="describe|it|test|@Test",
-     file_pattern="*.test.*",
-     context_lines=0
-   )
+   rg "describe|it|test|@Test" -g "*.test.*"
    ```
 
 2. **Coverage Gap Analysis**
@@ -80,18 +76,10 @@ Specialized context collector for test generation workflows that analyzes test c
 1. **Framework Identification**
    ```bash
    # Check package.json or requirements.txt
-   mcp__code-index__search_code_advanced(
-     pattern="jest|mocha|jasmine|pytest|unittest|rspec",
-     file_pattern="package.json|requirements.txt|Gemfile",
-     context_lines=2
-   )
+   rg "jest|mocha|jasmine|pytest|unittest|rspec" -g "package.json" -g "requirements.txt" -g "Gemfile" -C 2
 
    # Analyze existing test patterns
-   mcp__code-index__search_code_advanced(
-     pattern="describe\\(|it\\(|test\\(|def test_",
-     file_pattern="*.test.*",
-     context_lines=3
-   )
+   rg "describe\(|it\(|test\(|def test_" -g "*.test.*" -C 3
    ```
 
 2. **Convention Analysis**
@@ -207,33 +195,26 @@ Generate `test-context-package.json`:
 .workflow/{test_session_id}/.process/test-context-package.json
 ```
 
-## MCP Tools Usage
+## Native Tools Usage
 
 ### File Discovery
 ```bash
 # Test files
-mcp__code-index__find_files(pattern="*.test.*")
-mcp__code-index__find_files(pattern="*.spec.*")
+find . -name "*.test.*" -type f
+find . -name "*.spec.*" -type f
 
 # Implementation files
-mcp__code-index__find_files(pattern="*.ts")
-mcp__code-index__find_files(pattern="*.js")
+find . -name "*.ts" -type f
+find . -name "*.js" -type f
 ```
 
 ### Content Search
 ```bash
 # Test framework detection
-mcp__code-index__search_code_advanced(
-  pattern="jest|mocha|pytest",
-  file_pattern="package.json|requirements.txt"
-)
+rg "jest|mocha|pytest" -g "package.json" -g "requirements.txt"
 
 # Test pattern analysis
-mcp__code-index__search_code_advanced(
-  pattern="describe|it|test",
-  file_pattern="*.test.*",
-  context_lines=2
-)
+rg "describe|it|test" -g "*.test.*" -C 2
 ```
 
 ### Coverage Analysis
@@ -249,7 +230,7 @@ test_file_patterns=(
 
 # Search for test file
 for pattern in "${test_file_patterns[@]}"; do
-  if mcp__code-index__find_files(pattern="$pattern") | grep -q .; then
+  if [ -f "$pattern" ]; then
     echo "✅ Test exists: $pattern"
     break
   fi
@@ -262,10 +243,9 @@ done
 |-------|-------|------------|
 | Source session not found | Invalid source_session reference | Verify test session metadata |
 | No implementation summaries | Source session incomplete | Complete source session first |
-| MCP tools unavailable | MCP not configured | Fallback to bash find/grep |
 | No test framework detected | Missing test dependencies | Request user to specify framework |
 
-## Fallback Strategy (No MCP)
+## Native Tools Implementation
 
 ```bash
 # File discovery
@@ -287,8 +267,8 @@ done
 - `/workflow:test-gen` (Phase 3: Context Gathering)
 
 ### Calls
-- MCP code-index tools for analysis
-- Bash file operations for fallback
+- Ripgrep and find for file analysis
+- Bash file operations for coverage analysis
 
 ### Followed By
 - `/workflow:tools:test-concept-enhanced` - Analyzes context and plans test generation
@@ -296,7 +276,7 @@ done
 ## Success Criteria
 
 - ✅ Source session context loaded successfully
-- ✅ Test coverage gaps identified with MCP tools
+- ✅ Test coverage gaps identified with ripgrep
 - ✅ Test framework detected and documented
 - ✅ Valid test-context-package.json generated
 - ✅ All missing tests catalogued with priority

.claude/commands/workflow/tools/test-task-generate.md

@@ -146,9 +146,9 @@ Generate **TWO task JSON files**:
         "step": "load_existing_test_patterns",
         "action": "Study existing tests for pattern reference",
         "commands": [
-          "mcp__code-index__find_files(pattern=\"*.test.*\")",
+          "bash(find . -name \"*.test.*\" -type f)",
           "bash(# Read first 2 existing test files as examples)",
-          "bash(test_files=$(mcp__code-index__find_files(pattern=\"*.test.*\") | head -2))",
+          "bash(test_files=$(find . -name \"*.test.*\" -type f | head -2))",
           "bash(for f in $test_files; do echo \"=== $f ===\"&& cat \"$f\"; done)"
         ],
         "output_to": "existing_test_patterns",
@@ -282,11 +282,11 @@ Generate **TWO task JSON files**:
         "step": "analyze_test_coverage",
         "action": "Analyze test coverage and identify missing tests",
         "commands": [
-          "mcp__code-index__find_files(pattern=\"*.test.*\")",
-          "mcp__code-index__search_code_advanced(pattern=\"test|describe|it|def test_\", file_pattern=\"*.test.*\")",
+          "bash(find . -name \"*.test.*\" -type f)",
+          "bash(rg \"test|describe|it|def test_\" -g \"*.test.*\")",
           "bash(# Count implementation files vs test files)",
           "bash(impl_count=$(find [changed_files_dirs] -type f \\( -name '*.ts' -o -name '*.js' -o -name '*.py' \\) ! -name '*.test.*' 2>/dev/null | wc -l))",
-          "bash(test_count=$(mcp__code-index__find_files(pattern=\"*.test.*\") | wc -l))",
+          "bash(test_count=$(find . -name \"*.test.*\" -type f | wc -l))",
           "bash(echo \"Implementation files: $impl_count, Test files: $test_count\")"
         ],
         "output_to": "test_coverage_analysis",