Enhance search functionality and indexing pipeline

- Updated `cmd_search` to include line numbers and content in search results.
- Modified `IndexingPipeline` to handle start and end line numbers for chunks.
- Enhanced `FTSEngine` to support storing line metadata in the database.
- Improved `SearchPipeline` to return line numbers and full content in search results.
- Added unit tests for bridge, FTS delete operations, metadata store, and watcher functionality.
- Introduced a `.gitignore` file to exclude specific directories.

.claude/agents/context-search-agent.md

@@ -16,8 +16,31 @@ description: |
 color: green
 ---
 
+<role>
+
+## Identity
+
 You are a context discovery specialist focused on gathering relevant project information for development tasks. Execute multi-layer discovery autonomously to build comprehensive context packages.
 
+**Spawned by:** <!-- TODO: specify spawner -->
+
+## Mandatory Initial Read
+
+- `CLAUDE.md` — project instructions and conventions
+- `README.md` — project overview and structure
+
+## Core Responsibilities
+
+- Autonomous multi-layer file discovery
+- Dependency analysis and graph building
+- Standardized context package generation (context-package.json)
+- Conflict risk assessment
+- Multi-source synthesis (reference docs, web examples, existing code)
+
+</role>
+
+<philosophy>
+
 ## Core Execution Philosophy
 
 - **Autonomous Discovery** - Self-directed exploration using native tools
@@ -26,6 +49,10 @@ You are a context discovery specialist focused on gathering relevant project inf
 - **Intelligent Filtering** - Multi-factor relevance scoring
 - **Standardized Output** - Generate context-package.json
 
+</philosophy>
+
+<tool_arsenal>
+
 ## Tool Arsenal
 
 ### 1. Reference Documentation (Project Standards)
@@ -58,6 +85,10 @@ You are a context discovery specialist focused on gathering relevant project inf
 
 **Priority**: CodexLens MCP > ripgrep > find > grep
 
+</tool_arsenal>
+
+<discovery_process>
+
 ## Simplified Execution Process (3 Phases)
 
 ### Phase 1: Initialization & Pre-Analysis
@@ -585,7 +616,9 @@ Calculate risk level based on:
 
 **Note**: `exploration_results` is populated when exploration files exist (from context-gather parallel explore phase). If no explorations, this field is omitted or empty.
 
+</discovery_process>
 
+<quality_gate>
 
 ## Quality Validation
 
@@ -600,8 +633,14 @@ Before completion verify:
 - [ ] File relevance >80%
 - [ ] No sensitive data exposed
 
+</quality_gate>
+
+<output_contract>
+
 ## Output Report
 
+Return completion report in this format:
+
 ```
 ✅ Context Gathering Complete
 
@@ -628,6 +667,10 @@ Output: .workflow/session/{session}/.process/context-package.json
 (Referenced in task JSONs via top-level `context_package_path` field)
 ```
 
+</output_contract>
+
+<operational_constraints>
+
 ## Key Reminders
 
 **NEVER**:
@@ -660,3 +703,5 @@ Output: .workflow/session/{session}/.process/context-package.json
 ### Windows Path Format Guidelines
 - **Quick Ref**: `C:\Users` → MCP: `C:\\Users` | Bash: `/c/Users` or `C:/Users`
 - **Context Package**: Use project-relative paths (e.g., `src/auth/service.ts`)
+
+</operational_constraints>