feat: migrate to use MCP tools instead of helper scripts

prompts/pre-recon-code.txt

@@ -78,9 +78,13 @@ You are the **Code Intelligence Gatherer** and **Architectural Foundation Builde
 **Available Tools:**
 - **Task Agent (Code Analysis):** Your primary tool. Use it to ask targeted questions about the source code, trace authentication mechanisms, map attack surfaces, and understand architectural patterns. MANDATORY for all source code analysis.
 - **TodoWrite Tool:** Use this to create and manage your analysis task list. Create todo items for each phase and agent that needs execution. Mark items as "in_progress" when working on them and "completed" when done.
-- **Bash tool:** Your primary tool for executing shell commands. Use it for creating directories, copying files, and, most importantly, for **saving your final deliverable** by executing the `save_deliverable.js` script.
-  - **Saving Deliverable:** To save your work, you MUST use the following command. The script handles correct naming and validates output. It will print `{"status": "success"}` on success or `{"status": "error"}` on failure.
-    - **For your analysis report:** `node save_deliverable.js CODE_ANALYSIS 'your complete markdown report'`
+- **save_deliverable (MCP Tool):** Saves your final deliverable file with automatic validation.
+  - **Parameters:**
+    - `deliverable_type`: "CODE_ANALYSIS" (required)
+    - `content`: Your complete markdown report (required)
+  - **Returns:** `{ status: "success", filepath: "...", validated: true/false }` on success or `{ status: "error", message: "...", errorType: "...", retryable: true/false }` on failure
+  - **Usage:** Call the tool with your complete markdown report. The tool handles correct naming and file validation automatically.
+- **Bash tool:** Use for creating directories, copying files, and other shell commands as needed.
 </available_tools>
 
 <task_agent_strategy>
@@ -123,7 +127,7 @@ After Phase 1 completes, launch all three vulnerability-focused agents in parall
   - Create the `outputs/schemas/` directory using mkdir -p
   - Copy all discovered schema files to `outputs/schemas/` with descriptive names
   - Include schema locations in your attack surface analysis
-- Save complete analysis using: `node save_deliverable.js CODE_ANALYSIS 'your complete markdown report'`
+- Save complete analysis using the `save_deliverable` MCP tool with `deliverable_type: "CODE_ANALYSIS"` and your complete markdown report as the `content`
 
 **EXECUTION PATTERN:**
 1. **Use TodoWrite to create task list** tracking: Phase 1 agents, Phase 2 agents, and report synthesis
@@ -381,7 +385,7 @@ A component is **out-of-scope** if it **cannot** be invoked through the running
    - Phase 3: Synthesis and report generation completed
 
 2. **Deliverable Generation:** The following files must be successfully created:
-   - `deliverables/code_analysis_deliverable.md` (Created using save_deliverable script with CODE_ANALYSIS type)
+   - `deliverables/code_analysis_deliverable.md` (Created using save_deliverable MCP tool with CODE_ANALYSIS type)
    - `outputs/schemas/` directory with all discovered schema files copied (if any schemas found)
 
 3. **TodoWrite Completion:** All tasks in your todo list must be marked as completed