feat: migrate to Gemini CLI v0.11.0-nightly with native prompt support

## Major Changes

### Gemini CLI Integration (google-gemini/gemini-cli#11228)
- Migrate from wrapper scripts to native Gemini CLI v0.11.0-nightly
- Remove `-p` flag requirement for prompt strings
- Deprecate `gemini-wrapper` and `qwen-wrapper` scripts
- Update all commands and workflows to use direct CLI syntax

### Command Syntax Updates
- **Before**: `gemini -p "CONTEXT: @**/* prompt"`
- **After**: `gemini "CONTEXT: @**/* prompt"`
- Apply to all 70+ command files and workflow templates
- Maintain backward compatibility for Qwen fallback

### File Pattern Migration
- Replace `@{CLAUDE.md}` with `@CLAUDE.md`
- Replace `@{**/*}` with `@**/*`
- Update all file references to use direct @ notation
- Remove legacy brace syntax across all documentation

### Documentation Improvements
- Reorganize `intelligent-tools-strategy.md` structure
- Add Quick Start section with decision matrix
- Enhance `--include-directories` best practices
- Add comprehensive command templates and examples
- Improve navigation with clearer section hierarchy

### Files Modified (75+ files)
- Commands: All CLI commands updated (cli/, workflow/, task/, memory/)
- Workflows: Core strategy files and templates
- Agents: CLI execution agent and doc generator
- Templates: Planning roles and tech stack guides

## Breaking Changes
- Gemini CLI v0.11.0-nightly or later required
- Old wrapper scripts no longer supported
- Legacy `@{pattern}` syntax deprecated

## Migration Guide
Users should:
1. Update Gemini CLI to v0.11.0-nightly or later
2. Remove `-p` flag from existing commands
3. Update file patterns from `@{pattern}` to `@pattern`

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

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

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

@@ -79,11 +79,11 @@ The agent handles all phases internally.
 ## Command Template
 
 ```bash
-cd [directory] && ~/.claude/scripts/gemini-wrapper --all-files -p "
+cd [directory] && gemini -p "
 PURPOSE: [bug analysis goal]
 TASK: Systematic bug analysis and fix recommendations
 MODE: analysis
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md} [entire codebase in directory]
+CONTEXT: @CLAUDE.md @**/*CLAUDE.md [entire codebase in directory]
 EXPECTED: Root cause analysis, code path tracing, targeted fix suggestions
 RULES: $(cat ~/.claude/prompt-templates/bug-fix.md) | Bug: [description]
 "
@@ -111,11 +111,11 @@ RULES: $(cat ~/.claude/prompt-templates/bug-fix.md) | Bug: [description]
 
 **Standard Template Example**:
 ```bash
-cd . && ~/.claude/scripts/gemini-wrapper --all-files -p "
+cd . && gemini -p "
 PURPOSE: Debug authentication null pointer error
 TASK: Identify root cause and provide fix recommendations
 MODE: analysis
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}
+CONTEXT: @CLAUDE.md @**/*CLAUDE.md
 EXPECTED: Root cause, code path, minimal fix suggestion, impact assessment
 RULES: $(cat ~/.claude/prompt-templates/bug-fix.md) | Bug: null pointer in login flow
 "
@@ -123,11 +123,11 @@ RULES: $(cat ~/.claude/prompt-templates/bug-fix.md) | Bug: null pointer in login
 
 **Directory-Specific**:
 ```bash
-cd src/auth && ~/.claude/scripts/gemini-wrapper --all-files -p "
+cd src/auth && gemini -p "
 PURPOSE: Fix token validation failure
 TASK: Analyze token validation bug in auth module
 MODE: analysis
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}
+CONTEXT: @CLAUDE.md @**/*CLAUDE.md
 EXPECTED: Validation logic analysis, fix recommendation with minimal changes
 RULES: $(cat ~/.claude/prompt-templates/bug-fix.md) | Bug: token validation fails intermittently
 "
@@ -161,4 +161,4 @@ mcp__code-index__search_code_advanced(pattern="error|exception", file_pattern="*
 - Command templates and file patterns: see intelligent-tools-strategy.md (loaded in memory)
 - Scratchpad directory details: see workflow-architecture.md
 - Template path: `~/.claude/prompt-templates/bug-fix.md`
-- Always uses `--all-files` for comprehensive codebase context
+- Uses `@**/*` for in CONTEXT field for comprehensive codebase context

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

@@ -82,11 +82,11 @@ The agent handles all phases internally.
 ## Command Template
 
 ```bash
-cd [directory] && ~/.claude/scripts/gemini-wrapper --all-files -p "
+cd [directory] && gemini -p "
 PURPOSE: [analysis goal]
 TASK: Systematic code analysis and execution path tracing
 MODE: analysis
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md} [entire codebase in directory]
+CONTEXT: @CLAUDE.md @**/*CLAUDE.md [entire codebase in directory]
 EXPECTED: Execution trace, call flow diagram, debugging insights
 RULES: $(cat ~/.claude/prompt-templates/code-analysis.md) | Focus on [aspect]
 "
@@ -114,11 +114,11 @@ RULES: $(cat ~/.claude/prompt-templates/code-analysis.md) | Focus on [aspect]
 
 **Standard Template Example**:
 ```bash
-cd . && ~/.claude/scripts/gemini-wrapper --all-files -p "
+cd . && gemini -p "
 PURPOSE: Trace authentication execution flow
 TASK: Analyze complete auth flow from request to response
 MODE: analysis
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}
+CONTEXT: @CLAUDE.md @**/*CLAUDE.md
 EXPECTED: Step-by-step execution trace with call diagram, variable states
 RULES: $(cat ~/.claude/prompt-templates/code-analysis.md) | Focus on control flow
 "
@@ -126,11 +126,11 @@ RULES: $(cat ~/.claude/prompt-templates/code-analysis.md) | Focus on control flo
 
 **Directory-Specific Analysis**:
 ```bash
-cd src/auth && ~/.claude/scripts/gemini-wrapper --all-files -p "
+cd src/auth && gemini -p "
 PURPOSE: Understand JWT token validation logic
 TASK: Trace JWT validation from middleware to service layer
 MODE: analysis
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}
+CONTEXT: @CLAUDE.md @**/*CLAUDE.md
 EXPECTED: Validation flow diagram, token lifecycle analysis
 RULES: $(cat ~/.claude/prompt-templates/code-analysis.md) | Focus on security
 "
@@ -167,4 +167,4 @@ mcp__code-index__search_code_advanced(pattern="authenticate|login", file_pattern
 - Command templates and file patterns: see intelligent-tools-strategy.md (loaded in memory)
 - Scratchpad directory details: see workflow-architecture.md
 - Template path: `~/.claude/prompt-templates/code-analysis.md`
-- Always uses `--all-files` for comprehensive code context
+- Uses `@**/*` for in CONTEXT field for comprehensive code context

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

@@ -80,11 +80,11 @@ The agent handles all phases internally.
 ## Command Template
 
 ```bash
-cd [directory] && ~/.claude/scripts/gemini-wrapper --all-files -p "
+cd [directory] && gemini -p "
 PURPOSE: [planning goal from topic]
 TASK: Comprehensive planning and architecture analysis
 MODE: analysis
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md} [entire codebase in directory]
+CONTEXT: @CLAUDE.md @**/*CLAUDE.md [entire codebase in directory]
 EXPECTED: Strategic insights, implementation recommendations, key decisions
 RULES: $(cat ~/.claude/prompt-templates/plan.md) | Focus on [topic area]
 "
@@ -112,11 +112,11 @@ RULES: $(cat ~/.claude/prompt-templates/plan.md) | Focus on [topic area]
 
 **Standard Template Example**:
 ```bash
-cd . && ~/.claude/scripts/gemini-wrapper --all-files -p "
+cd . && gemini -p "
 PURPOSE: Design user dashboard architecture
 TASK: Plan dashboard component structure and data flow
 MODE: analysis
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}
+CONTEXT: @CLAUDE.md @**/*CLAUDE.md
 EXPECTED: Architecture recommendations, component design, data flow diagram
 RULES: $(cat ~/.claude/prompt-templates/plan.md) | Focus on scalability
 "
@@ -124,11 +124,11 @@ RULES: $(cat ~/.claude/prompt-templates/plan.md) | Focus on scalability
 
 **Directory-Specific Planning**:
 ```bash
-cd src/api && ~/.claude/scripts/gemini-wrapper --all-files -p "
+cd src/api && gemini -p "
 PURPOSE: Plan API refactoring strategy
 TASK: Analyze current API structure and recommend improvements
 MODE: analysis
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}
+CONTEXT: @CLAUDE.md @**/*CLAUDE.md
 EXPECTED: Refactoring roadmap, breaking change analysis, migration plan
 RULES: $(cat ~/.claude/prompt-templates/plan.md) | Maintain backward compatibility
 "
@@ -165,4 +165,4 @@ rg "architecture|design" --files-with-matches
 - Command templates and file patterns: see intelligent-tools-strategy.md (loaded in memory)
 - Scratchpad directory details: see workflow-architecture.md
 - Template path: `~/.claude/prompt-templates/plan.md`
-- Always uses `--all-files` for comprehensive project context
+- Uses `@**/*` for in CONTEXT field for comprehensive project context