refactor(agents): remove code-index MCP dependencies

Remove references to mcp__code-index MCP tool and simplify context discovery to use native search tools (ripgrep, find) with MCP Exa for external research.

Changes:
- action-planning-agent.md: Remove code-index from capabilities and examples
- cli-execution-agent.md: Remove MCP code-index discovery section, update to use ripgrep/find only
- code-developer.md: Minor documentation updates
- task-json-agent-mode.txt: Remove code-index references
- task-json-cli-mode.txt: Remove code-index references
- workflow-architecture.md: Update MCP integration documentation

Rationale:
- Simplify dependency stack
- Native tools (rg, find) provide sufficient file discovery capabilities
- MCP Exa remains for external research (best practices, documentation)
- Reduces maintenance overhead and improves reliability

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

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

.claude/agents/action-planning-agent.md

@@ -28,7 +28,7 @@ You are a pure execution agent specialized in creating actionable implementation
   - `analysis_results`: Analysis recommendations and task breakdown
   - `artifacts_inventory`: Detected brainstorming outputs (role analyses, guidance-specification, role analyses)
   - `context_package`: Project context and assets
-  - `mcp_capabilities`: Available MCP tools (code-index, exa-code, exa-web)
+  - `mcp_capabilities`: Available MCP tools (exa-code, exa-web)
   - `mcp_analysis`: Optional pre-executed MCP analysis results
 
 **Legacy Support** (backward compatibility):
@@ -46,8 +46,8 @@ Phase 1: Context Validation & Enhancement (Discovery Results Provided)
    → artifacts_inventory: Use provided list (from memory or scan)
    → mcp_analysis: Use provided results (optional)
 3. Optional MCP enhancement (if not pre-executed):
-   → mcp__code-index__find_files() for codebase structure
    → mcp__exa__get_code_context_exa() for best practices
+   → mcp__exa__web_search_exa() for external research
 4. Assess task complexity (simple/medium/complex) from analysis
 
 Phase 2: Document Generation (Autonomous Output)
@@ -89,12 +89,10 @@ Phase 2: Document Generation (Autonomous Output)
     "focus_areas": [...]
   },
   "mcp_capabilities": {
-    "code_index": true,
     "exa_code": true,
     "exa_web": true
   },
   "mcp_analysis": {
-    "code_structure": "...",
     "external_research": "..."
   }
 }
@@ -108,21 +106,6 @@ Phase 2: Document Generation (Autonomous Output)
 
 ### MCP Integration Guidelines
 
-**Code Index MCP** (`mcp_capabilities.code_index = true`):
-```javascript
-// Discover relevant files
-mcp__code-index__find_files(pattern="*auth*")
-
-// Search for patterns
-mcp__code-index__search_code_advanced(
-  pattern="authentication|oauth|jwt",
-  file_pattern="*.{ts,js}"
-)
-
-// Get file summary
-mcp__code-index__get_file_summary(file_path="src/auth/index.ts")
-```
-
 **Exa Code Context** (`mcp_capabilities.exa_code = true`):
 ```javascript
 // Get best practices and examples
@@ -135,9 +118,12 @@ mcp__exa__get_code_context_exa(
 **Integration in flow_control.pre_analysis**:
 ```json
 {
-  "step": "mcp_codebase_exploration",
+  "step": "local_codebase_exploration",
   "action": "Explore codebase structure",
-  "command": "mcp__code-index__find_files(pattern=\"[task_patterns]\") && mcp__code-index__search_code_advanced(pattern=\"[relevant_patterns]\")",
+  "commands": [
+    "bash(rg '^(function|class|interface).*[task_keyword]' --type ts -n --max-count 15)",
+    "bash(find . -name '*[task_keyword]*' -type f | grep -v node_modules | head -10)"
+  ],
   "output_to": "codebase_structure"
 }
 ```

.claude/agents/cli-execution-agent.md

@@ -1,23 +1,23 @@
 ---
 name: cli-execution-agent
 description: |
-  Intelligent CLI execution agent with automated context discovery and smart tool selection. Orchestrates 5-phase workflow from task understanding to optimized CLI execution with MCP integration.
+  Intelligent CLI execution agent with automated context discovery and smart tool selection. Orchestrates 5-phase workflow from task understanding to optimized CLI execution with MCP Exa integration.
 
   Examples:
   - Context: User provides task without context
     user: "Implement user authentication"
     assistant: "I'll discover relevant context, enhance the task description, select optimal tool, and execute"
-    commentary: Agent autonomously discovers context via MCP code-index, researches best practices, builds enhanced prompt, selects Codex for complex implementation
+    commentary: Agent autonomously discovers context via ripgrep/find, researches best practices via MCP Exa, builds enhanced prompt, selects Codex for complex implementation
 
   - Context: User provides analysis task
     user: "Analyze API architecture patterns"
     assistant: "I'll gather API-related files, analyze patterns, and execute with Gemini for comprehensive analysis"
-    commentary: Agent discovers API files, identifies patterns, selects Gemini for architecture analysis
+    commentary: Agent discovers API files via local search, identifies patterns, selects Gemini for architecture analysis
 
   - Context: User provides task with session context
     user: "Execute IMPL-001 from active workflow"
     assistant: "I'll load task context, discover implementation files, enhance requirements, and execute"
-    commentary: Agent loads task JSON, discovers code context, routes output to workflow session
+    commentary: Agent loads task JSON, discovers code context via local search, routes output to workflow session
 color: purple
 ---
 
@@ -88,7 +88,7 @@ Score < 2 → Simple
 
 ## Phase 2: Context Discovery
 
-### Multi-Tool Parallel Strategy
+### Context Discovery Strategy
 
 **1. Project Structure Analysis**:
 ```bash
@@ -96,27 +96,7 @@ Score < 2 → Simple
 ```
 Output: Module hierarchy and organization
 
-**2. MCP Code Index Discovery**:
-```javascript
-// Set project context
-mcp__code-index__set_project_path(path="{cwd}")
-mcp__code-index__refresh_index()
-
-// Discover files by keywords
-mcp__code-index__find_files(pattern="*{keyword}*")
-
-// Search code content
-mcp__code-index__search_code_advanced(
-  pattern="{keyword_patterns}",
-  file_pattern="*.{ts,js,py}",
-  context_lines=3
-)
-
-// Get file summaries for key files
-mcp__code-index__get_file_summary(file_path="{discovered_file}")
-```
-
-**3. Content Search (ripgrep fallback)**:
+**2. Content Search (ripgrep)**:
 ```bash
 # Function/class definitions
 rg "^(function|def|func|class|interface).*{keyword}" \
@@ -130,7 +110,7 @@ find . \( -name "*{keyword}*test*" -o -name "*{keyword}*spec*" \) \
    -type f | grep -E "\.(js|ts|py|go)$" | head -10
 ```
 
-**4. External Research (MCP Exa - Optional)**:
+**3. External Research (MCP Exa - Optional)**:
 ```javascript
 // Best practices for complex tasks
 mcp__exa__get_code_context_exa(
@@ -438,30 +418,6 @@ if (activeSession.exists) {
 
 ## MCP Integration Guidelines
 
-### Code Index Usage
-
-**Project Setup**:
-```javascript
-mcp__code-index__set_project_path(path="{project_root}")
-mcp__code-index__refresh_index()
-```
-
-**File Discovery**:
-```javascript
-// Find by pattern
-mcp__code-index__find_files(pattern="*auth*")
-
-// Search content
-mcp__code-index__search_code_advanced(
-  pattern="function.*authenticate",
-  file_pattern="*.ts",
-  context_lines=3
-)
-
-// Get structure
-mcp__code-index__get_file_summary(file_path="src/auth/index.ts")
-```
-
 ### Exa Research Usage
 
 **Best Practices**:
@@ -484,13 +440,11 @@ mcp__exa__get_code_context_exa(
 
 ### Graceful Degradation
 
-**MCP Unavailable**:
+**MCP Exa Unavailable**:
 ```bash
-# Fallback to ripgrep + find
-if ! mcp__code-index__find_files; then
-  find . -name "*{keyword}*" -type f | grep -v node_modules
-  rg "{keyword}" --type ts --max-count 20
-fi
+# Fallback to local search only
+find . -name "*{keyword}*" -type f | grep -v node_modules
+rg "{keyword}" --type ts --max-count 20
 ```
 
 **Tool Unavailable**:

.claude/agents/code-developer.md

@@ -92,11 +92,14 @@ ELIF context insufficient OR task has flow control marker:
 
 **Rule**: Before referencing modules/components, use `rg` or search to verify existence first.
 
-**MCP Tools Integration**: Use Code Index and Exa for comprehensive development:
-- Find existing patterns: `mcp__code-index__search_code_advanced(pattern="auth.*function")`
-- Locate files: `mcp__code-index__find_files(pattern="src/**/*.ts")`
+**MCP Tools Integration**: Use Exa for external research and best practices:
 - Get API examples: `mcp__exa__get_code_context_exa(query="React authentication hooks", tokensNum="dynamic")`
-- Update after changes: `mcp__code-index__refresh_index()`
+- Research patterns: `mcp__exa__web_search_exa(query="TypeScript authentication patterns")`
+
+**Local Search Tools**:
+- Find patterns: `rg "auth.*function" --type ts -n`
+- Locate files: `find . -name "*.ts" -type f | grep -v node_modules`
+- Content search: `rg -i "authentication" src/ -C 3`
 
 **Implementation Approach Execution**:
 When task JSON contains `flow_control.implementation_approach` array:

.claude/workflows/cli-templates/prompts/workflow/task-json-agent-mode.txt

@@ -52,9 +52,12 @@ Task JSON Schema - Agent Mode (No Command Field)
         "on_error": "fail"
       },
       {
-        "step": "mcp_codebase_exploration",
-        "action": "Explore codebase using MCP",
-        "command": "mcp__code-index__find_files(pattern=\"{file_pattern}\") && mcp__code-index__search_code_advanced(pattern=\"{search_pattern}\")",
+        "step": "local_codebase_exploration",
+        "action": "Explore codebase using local search",
+        "commands": [
+          "bash(rg '^(function|class|interface).*{keyword}' --type ts -n --max-count 15)",
+          "bash(find . -name '*{keyword}*' -type f | grep -v node_modules | head -10)"
+        ],
         "output_to": "codebase_structure",
         "on_error": "skip_optional"
       }

.claude/workflows/cli-templates/prompts/workflow/task-json-cli-mode.txt

@@ -52,9 +52,12 @@ Task JSON Schema - CLI Execute Mode (With Command Field)
         "on_error": "fail"
       },
       {
-        "step": "mcp_codebase_exploration",
-        "action": "Explore codebase using MCP",
-        "command": "mcp__code-index__find_files(pattern=\"{file_pattern}\")",
+        "step": "local_codebase_exploration",
+        "action": "Explore codebase using local search",
+        "commands": [
+          "bash(rg '^(function|class|interface).*{keyword}' --type ts -n --max-count 15)",
+          "bash(find . -name '*{keyword}*' -type f | grep -v node_modules | head -10)"
+        ],
         "output_to": "codebase_structure",
         "on_error": "skip_optional"
       }

.claude/workflows/workflow-architecture.md

@@ -343,9 +343,12 @@ The `[FLOW_CONTROL]` marker indicates that a task or prompt contains flow contro
       "on_error": "skip_optional"
     },
     {
-      "step": "mcp_codebase_exploration",
-      "action": "Explore codebase using MCP",
-      "command": "mcp__code-index__find_files(pattern=\"*.ts\") && mcp__code-index__search_code_advanced(pattern=\"auth\")",
+      "step": "local_codebase_exploration",
+      "action": "Explore codebase using local search",
+      "commands": [
+        "bash(rg '^(function|class|interface).*auth' --type ts -n --max-count 15)",
+        "bash(find . -name '*auth*' -type f | grep -v node_modules | head -10)"
+      ],
       "output_to": "codebase_structure"
     }
   ],
@@ -416,7 +419,7 @@ The `[FLOW_CONTROL]` marker indicates that a task or prompt contains flow contro
 **Command Types Supported**:
 - **Bash commands**: `bash(command)` - Any shell command
 - **Tool calls**: `Read(file)`, `Glob(pattern)`, `Grep(pattern)`
-- **MCP tools**: `mcp__code-index__find_files()`, `mcp__exa__get_code_context_exa()`
+- **MCP tools**: `mcp__exa__get_code_context_exa()`, `mcp__exa__web_search_exa()`
 - **CLI commands**: `gemini`, `qwen`, `codex --full-auto exec`
 
 **Example**:
@@ -541,8 +544,6 @@ codex --full-auto exec "task" resume --last --skip-git-repo-check -s danger-full
 - `bash(command)` - Execute bash command
 
 **MCP Tools**:
-- `mcp__code-index__find_files(pattern="*.ts")` - Find files using code index
-- `mcp__code-index__search_code_advanced(pattern="auth")` - Search code patterns
 - `mcp__exa__get_code_context_exa(query="...")` - Get code context from Exa
 - `mcp__exa__web_search_exa(query="...")` - Web search via Exa