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/chat.md

@@ -27,7 +27,6 @@ Direct Q&A interaction with CLI tools for codebase analysis. **Analysis only - d
 - `--agent` - Use cli-execution-agent for automated context discovery (5-phase intelligent mode)
 - `--tool <codex|gemini|qwen>` - Select CLI tool (default: gemini, ignored in agent mode)
 - `--enhance` - Enhance inquiry with `/enhance-prompt` first
-- `--all-files` - Include entire codebase in context
 - `--save-session` - Save interaction to workflow session
 
 ## Execution Flow
@@ -36,7 +35,7 @@ Direct Q&A interaction with CLI tools for codebase analysis. **Analysis only - d
 
 1. Parse tool selection (default: gemini)
 2. If `--enhance`: Execute `/enhance-prompt` to expand user intent
-3. Assemble context: `@{CLAUDE.md}` + user-specified files or `--all-files`
+3. Assemble context: `@CLAUDE.md` + user-specified files or `@**/*` for entire codebase
 4. Execute CLI tool with assembled context (read-only, analysis mode)
 5. Return explanations and insights (NO code changes)
 6. Optionally save to workflow session
@@ -54,7 +53,6 @@ Task(
     Task: ${inquiry}
     Mode: analyze (Q&A)
     Tool Preference: ${tool_flag || 'auto-select'}
-    ${all_files_flag ? 'Scope: all-files' : ''}
 
     Agent will autonomously:
     - Discover files relevant to the question
@@ -69,20 +67,20 @@ The agent handles all phases internally.
 
 ## Context Assembly
 
-**Always included**: `@{CLAUDE.md,**/*CLAUDE.md}` (project guidelines)
+**Always included**: `@CLAUDE.md @**/*CLAUDE.md` (project guidelines)
 
 **Optional**:
 - User-explicit files from inquiry keywords
-- `--all-files` flag includes entire codebase (`--all-files` wrapper parameter)
+- Use `@**/*` in CONTEXT for entire codebase
 
 For targeted analysis, use `rg` or MCP tools to discover relevant files first, then build precise CONTEXT field.
 
 ## Command Template
 
 ```bash
-cd . && ~/.claude/scripts/gemini-wrapper -p "
+cd . && gemini -p "
 INQUIRY: [user question]
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md} [inferred or --all-files]
+CONTEXT: @CLAUDE.md,**/*CLAUDE.md [inferred files or @**/* for all files]
 MODE: analysis
 RESPONSE: Direct answer, explanation, insights (NO code modification)
 "
@@ -110,7 +108,7 @@ RESPONSE: Direct answer, explanation, insights (NO code modification)
 
 **Architecture Question**:
 ```bash
-/cli:chat --tool qwen "how does React component optimization work here"
+/cli:chat --tool qwen -p "how does React component optimization work here"
 # Executes: Qwen architecture analysis
 # Returns: Component structure explanation, optimization patterns used
 ```
@@ -130,13 +128,6 @@ RESPONSE: Direct answer, explanation, insights (NO code modification)
 # Returns: Detailed explanation of login flow and potential issues
 ```
 
-**Broad Context**:
-```bash
-/cli:chat --all-files "find all API endpoints"
-# Executes: Analysis across entire codebase
-# Returns: List and explanation of API endpoints (NO code generation)
-```
-
 ## Output Routing
 
 **Output Destination Logic**: