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/workflow/review.md

@@ -99,10 +99,10 @@ After bash validation, the model takes control to:
      ```
    - Use Gemini for security analysis:
      ```bash
-     cd .workflow/${sessionId} && ~/.claude/scripts/gemini-wrapper -p "
+     cd .workflow/${sessionId} && gemini -p "
      PURPOSE: Security audit of completed implementation
      TASK: Review code for security vulnerabilities, insecure patterns, auth/authz issues
-     CONTEXT: @{.summaries/IMPL-*.md,../..,../../CLAUDE.md}
+     CONTEXT: @.summaries/IMPL-*.md,../.. @../../CLAUDE.md
      EXPECTED: Security findings report with severity levels
      RULES: Focus on OWASP Top 10, authentication, authorization, data validation, injection risks
      " --approval-mode yolo
@@ -111,10 +111,10 @@ After bash validation, the model takes control to:
    **Architecture Review** (`--type=architecture`):
    - Use Qwen for architecture analysis:
      ```bash
-     cd .workflow/${sessionId} && ~/.claude/scripts/qwen-wrapper -p "
+     cd .workflow/${sessionId} && qwen -p "
      PURPOSE: Architecture compliance review
      TASK: Evaluate adherence to architectural patterns, identify technical debt, review design decisions
-     CONTEXT: @{.summaries/IMPL-*.md,../..,../../CLAUDE.md}
+     CONTEXT: @.summaries/IMPL-*.md,../.. @../../CLAUDE.md
      EXPECTED: Architecture assessment with recommendations
      RULES: Check for patterns, separation of concerns, modularity, scalability
      " --approval-mode yolo
@@ -123,10 +123,10 @@ After bash validation, the model takes control to:
    **Quality Review** (`--type=quality`):
    - Use Gemini for code quality:
      ```bash
-     cd .workflow/${sessionId} && ~/.claude/scripts/gemini-wrapper -p "
+     cd .workflow/${sessionId} && gemini -p "
      PURPOSE: Code quality and best practices review
      TASK: Assess code readability, maintainability, adherence to best practices
-     CONTEXT: @{.summaries/IMPL-*.md,../..,../../CLAUDE.md}
+     CONTEXT: @.summaries/IMPL-*.md,../.. @../../CLAUDE.md
      EXPECTED: Quality assessment with improvement suggestions
      RULES: Check for code smells, duplication, complexity, naming conventions
      " --approval-mode yolo
@@ -143,10 +143,10 @@ After bash validation, the model takes control to:
      ' {} \;
 
      # Check implementation summaries against requirements
-     cd .workflow/${sessionId} && ~/.claude/scripts/gemini-wrapper -p "
+     cd .workflow/${sessionId} && gemini -p "
      PURPOSE: Verify all requirements and acceptance criteria are met
      TASK: Cross-check implementation summaries against original requirements
-     CONTEXT: @{.task/IMPL-*.json,.summaries/IMPL-*.md,../..,../../CLAUDE.md}
+     CONTEXT: @.task/IMPL-*.json,.summaries/IMPL-*.md,../.. @../../CLAUDE.md
      EXPECTED:
      - Requirements coverage matrix
      - Acceptance criteria verification

.claude/commands/workflow/tdd-verify.md

@@ -3,7 +3,7 @@ name: tdd-verify
 description: Verify TDD workflow compliance and generate quality report
 
 argument-hint: "[optional: WFS-session-id]"
-allowed-tools: SlashCommand(*), TodoWrite(*), Read(*), Bash(gemini-wrapper:*)
+allowed-tools: SlashCommand(*), TodoWrite(*), Read(*), Bash(gemini:*)
 ---
 
 # TDD Verification Command (/workflow:tdd-verify)
@@ -94,7 +94,7 @@ find .workflow/{sessionId}/.task/ -name '*.json' -exec jq -r '.meta.agent' {} \;
 **Gemini analysis for comprehensive TDD compliance report**
 
 ```bash
-cd project-root && ~/.claude/scripts/gemini-wrapper -p "
+cd project-root && gemini -p "
 PURPOSE: Generate TDD compliance report
 TASK: Analyze TDD workflow execution and generate quality report
 CONTEXT: @{.workflow/{sessionId}/.task/*.json,.workflow/{sessionId}/.summaries/*,.workflow/{sessionId}/.process/tdd-cycle-report.md}

.claude/commands/workflow/test-cycle-execute.md

@@ -226,11 +226,11 @@ Iteration N (managed by test-cycle-execute orchestrator):
 
 #### CLI Analysis Command (executed by orchestrator)
 ```bash
-cd {project_root} && ~/.claude/scripts/gemini-wrapper -p "
+cd {project_root} && gemini -p "
 PURPOSE: Analyze test failures and generate fix strategy
 TASK: Review test failures and identify root causes
 MODE: analysis
-CONTEXT: @{test files, implementation files}
+CONTEXT: @test files @ implementation files
 
 [Test failure context and requirements...]
 

.claude/commands/workflow/tools/task-generate-tdd.md

@@ -2,7 +2,7 @@
 name: task-generate-tdd
 description: Generate TDD task chains with Red-Green-Refactor dependencies
 argument-hint: "--session WFS-session-id [--agent]"
-allowed-tools: Read(*), Write(*), Bash(gemini-wrapper:*), TodoWrite(*)
+allowed-tools: Read(*), Write(*), Bash(gemini:*), TodoWrite(*)
 ---
 
 # TDD Task Generation Command

.claude/commands/workflow/tools/task-generate.md

@@ -256,7 +256,7 @@ This enhanced 5-field schema embeds all necessary context, artifacts, and execut
         "action": "Analyze existing code patterns and identify modification targets",
         "commands": [
           "bash(cd \"[focus_paths]\")",
-          "bash(~/.claude/scripts/gemini-wrapper -p \"PURPOSE: Identify modification targets TASK: Analyze '[title]' and locate specific files/functions/lines to modify CONTEXT: [synthesis_specification] [individual_artifacts] EXPECTED: Code locations in format 'file:function:lines' RULES: Prioritize synthesis-specification.md, identify exact modification points\")"
+          "bash(gemini \"PURPOSE: Identify modification targets TASK: Analyze '[title]' and locate specific files/functions/lines to modify CONTEXT: [synthesis_specification] [individual_artifacts] EXPECTED: Code locations in format 'file:function:lines' RULES: Prioritize synthesis-specification.md, identify exact modification points\")"
         ],
         "output_to": "task_context_with_targets",
         "on_error": "fail"

.claude/commands/workflow/tools/test-concept-enhanced.md

@@ -48,7 +48,7 @@ Specialized analysis tool for test generation workflows that uses Gemini to anal
 
 **Tool Configuration**:
 ```bash
-cd .workflow/{test_session_id}/.process && ~/.claude/scripts/gemini-wrapper -p "
+cd .workflow/{test_session_id}/.process && gemini -p "
 PURPOSE: Analyze test coverage gaps and design comprehensive test generation strategy
 TASK: Study implementation context, existing tests, and generate test requirements for missing coverage
 MODE: analysis

.claude/commands/workflow/tools/test-task-generate.md

@@ -198,7 +198,7 @@ Generate **TWO task JSON files**:
         "Codex generates comprehensive test suite",
         "Codex validates test syntax and executability"
       ],
-      "command": "bash(codex -C [focus_paths] --full-auto exec \"PURPOSE: Generate comprehensive test suite TASK: Create test files based on TEST_ANALYSIS_RESULTS.md section 5 MODE: write CONTEXT: @{.workflow/WFS-test-[session]/.process/TEST_ANALYSIS_RESULTS.md,.workflow/WFS-test-[session]/.process/test-context-package.json} EXPECTED: All test files with happy path, error handling, edge cases, integration tests RULES: Follow test framework conventions, ensure tests are executable\" --skip-git-repo-check -s danger-full-access)",
+      "command": "bash(codex -C [focus_paths] --full-auto exec \"PURPOSE: Generate comprehensive test suite TASK: Create test files based on TEST_ANALYSIS_RESULTS.md section 5 MODE: write CONTEXT: @.workflow/WFS-test-[session]/.process/TEST_ANALYSIS_RESULTS.md @.workflow/WFS-test-[session]/.process/test-context-package.json EXPECTED: All test files with happy path, error handling, edge cases, integration tests RULES: Follow test framework conventions, ensure tests are executable\" --skip-git-repo-check -s danger-full-access)",
       "depends_on": [],
       "output": "test_generation"
     }],
@@ -323,7 +323,7 @@ Generate **TWO task JSON files**:
           "cycle_pattern": "test → gemini_diagnose → manual_fix (or codex if needed) → retest",
           "tools": {
             "test_execution": "bash(test_command)",
-            "diagnosis": "gemini-wrapper (MODE: analysis, uses bug-fix template)",
+            "diagnosis": "gemini (MODE: analysis, uses bug-fix template)",
             "fix_application": "manual (default) or codex exec resume --last (if explicitly needed)",
             "verification": "bash(test_command) + regression_check"
           },
@@ -354,11 +354,11 @@ Generate **TWO task JSON files**:
         "      * Source files from focus_paths",
         "      * Implementation summaries from source session",
         "    - Execute Gemini analysis with bug-fix template:",
-        "      bash(cd .workflow/WFS-test-[session]/.process && ~/.claude/scripts/gemini-wrapper --all-files -p \"",
+        "      bash(cd .workflow/WFS-test-[session]/.process && gemini \"",
         "      PURPOSE: Diagnose test failure iteration [N] and propose minimal fix",
         "      TASK: Systematic bug analysis and fix recommendations for test failure",
         "      MODE: analysis",
-        "      CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}",
+        "      CONTEXT: @CLAUDE.md,**/*CLAUDE.md",
         "               Test output: [test_failures]",
         "               Source files: [focus_paths]",
         "               Implementation: [implementation_context]",