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/scripts/update_module_claude.sh

@@ -88,8 +88,7 @@ update_module_claude() {
     
     # Use unified template for all modules
     local template_path="$HOME/.claude/workflows/cli-templates/prompts/memory/claude-module-unified.txt"
-    local analysis_strategy="--all-files"
-    
+
     # Prepare logging info
     local module_name=$(basename "$module_path")
 
@@ -131,8 +130,10 @@ update_module_claude() {
 
     $template_content
 
-    $update_context"
-    
+    $update_context
+
+    CONTEXT: @**/*"
+
     # Execute update
     local start_time=$(date +%s)
     echo "   🔄 Starting update..."
@@ -146,10 +147,11 @@ update_module_claude() {
         - Path: $module_path
         - Tool: $tool"
 
-        # Execute with selected tool (always use --all-files)
+        # Execute with selected tool
+        # NOTE: Prompt is passed via -p flag for gemini/qwen, first parameter for codex
         case "$tool" in
             qwen)
-                qwen --all-files --yolo -p "$final_prompt" 2>&1
+                qwen -p "$final_prompt" --yolo 2>&1
                 tool_result=$?
                 ;;
             codex)
@@ -157,7 +159,7 @@ update_module_claude() {
                 tool_result=$?
                 ;;
             gemini|*)
-                gemini --all-files --yolo -p "$final_prompt" 2>&1
+                gemini -p "$final_prompt" --yolo 2>&1
                 tool_result=$?
                 ;;
         esac