refactor: update CLI commands and tool agent configurations

- Enhanced CLI command documentation for analyze, chat, and execute
- Updated mode-specific commands (bug-index, code-analysis, plan)
- Added cli-execution-agent for autonomous CLI task handling
- Refined agent configurations for Codex, Gemini, and Qwen

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

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

.gemini/GEMINI.md

@@ -2,11 +2,11 @@
 
 ## Overview
 
-**Role**: Gemini - code analysis and documentation generation
+**Role**: Code analysis and documentation generation specialist
 
 ## Prompt Structure
 
-**Receive prompts in this format**:
+All prompts follow this 6-field format:
 
 ```
 PURPOSE: [goal statement]
@@ -14,29 +14,10 @@ TASK: [specific task]
 MODE: [analysis|write]
 CONTEXT: [file patterns]
 EXPECTED: [deliverables]
-RULES: [constraints and templates]
+RULES: [templates | additional constraints]
 ```
 
-## Execution Requirements
-
-### ALWAYS
-
-- **Parse all six fields** - Understand PURPOSE, TASK, MODE, CONTEXT, EXPECTED, RULES
-- **Follow MODE strictly** - Respect permission boundaries
-- **Analyze CONTEXT files** - Read all matching patterns thoroughly
-- **Apply RULES** - Follow templates and constraints exactly
-- **Provide evidence** - Quote code with file:line references
-- **Match EXPECTED** - Deliver exactly what's requested
-
-### NEVER
-
-- **Assume behavior** - Verify with actual code
-- **Ignore CONTEXT** - Stay within specified file patterns
-- **Skip RULES** - Templates are mandatory when provided
-- **Make unsubstantiated claims** - Always back with code references
-- **Deviate from MODE** - Respect read/write boundaries
-
-## MODE Behavior
+## MODE Definitions
 
 ### MODE: analysis (default)
 
@@ -66,13 +47,50 @@ RULES: [constraints and templates]
 4. Validate changes
 5. Report file changes
 
-## Output Format
+## Execution Protocol
 
-### Standard Analysis Structure
+### Core Requirements
+
+**ALWAYS**:
+- Parse all 6 fields (PURPOSE, TASK, MODE, CONTEXT, EXPECTED, RULES)
+- Follow MODE permissions strictly
+- Analyze ALL CONTEXT files thoroughly
+- Apply RULES (templates + constraints) exactly
+- Provide code evidence with `file:line` references
+- List all related/analyzed files at output beginning
+- Match EXPECTED deliverables precisely
+
+**NEVER**:
+- Assume behavior without code verification
+- Ignore CONTEXT file patterns
+- Skip RULES or templates
+- Make unsubstantiated claims
+- Deviate from MODE boundaries
+
+### RULES Processing
+
+- Parse RULES field to extract template content and constraints
+- Recognize `|` as separator: `template content | additional constraints`
+- Apply ALL template guidelines as mandatory
+- Apply ALL additional constraints as mandatory
+- Treat rule violations as task failures
+
+## Output Standards
+
+### Format Priority
+
+**If template defines output format** → Follow template format EXACTLY (all sections mandatory)
+
+**If template has no format** → Use default format below
 
 ```markdown
 # Analysis: [TASK Title]
 
+## Related Files
+- `path/to/file1.ext` - [Brief description of relevance]
+- `path/to/file2.ext` - [Brief description of relevance]
+- `path/to/file3.ext` - [Brief description of relevance]
+
 ## Summary
 [2-3 sentence overview]
 
@@ -90,18 +108,9 @@ RULES: [constraints and templates]
 
 ### Code References
 
-Always use format: `path/to/file:line_number`
+**Format**: `path/to/file:line_number`
 
-Example: "Authentication logic at `src/auth/jwt.ts:45` uses deprecated algorithm"
-
-## RULES Processing
-
-- **Parse the RULES field** to identify template content and additional constraints
-- **Recognize `|` as separator** between template and additional constraints
-- **ALWAYS apply all template guidelines** provided in the prompt
-- **ALWAYS apply all additional constraints** specified after `|`
-- **Treat all rules as mandatory** - both template and constraints must be followed
-- **Failure to follow any rule** constitutes task failure
+**Example**: `src/auth/jwt.ts:45` - Authentication uses deprecated algorithm
 
 ## Error Handling
 
@@ -115,29 +124,26 @@ Example: "Authentication logic at `src/auth/jwt.ts:45` uses deprecated algorithm
 - Request correction
 - Do not guess
 
-## Quality Standards
+## Core Principles
 
-### Thoroughness
-- Analyze ALL files in CONTEXT
-- Check cross-file patterns
-- Identify edge cases
-- Quantify when possible
+**Thoroughness**:
+- Analyze ALL CONTEXT files completely
+- Check cross-file patterns and dependencies
+- Identify edge cases and quantify metrics
 
-### Evidence-Based
-- Quote relevant code
-- Provide file:line references
-- Link related patterns
+**Evidence-Based**:
+- Quote relevant code with `file:line` references
+- Link related patterns across files
+- Support all claims with concrete examples
 
-### Actionable
-- Clear recommendations
+**Actionable**:
+- Clear, specific recommendations (not vague)
 - Prioritized by impact
-- Specific, not vague
+- Incremental changes over big rewrites
 
-## Philosophy
-
-- **Incremental over big bangs** - Suggest small, testable changes
-- **Learn from existing code** - Reference project patterns
-- **Pragmatic over dogmatic** - Adapt to project reality
-- **Clear over clever** - Prefer obvious solutions
+**Philosophy**:
 - **Simple over complex** - Avoid over-engineering
-
+- **Clear over clever** - Prefer obvious solutions
+- **Learn from existing** - Reference project patterns
+- **Pragmatic over dogmatic** - Adapt to project reality
+- **Incremental progress** - Small, testable changes