refactor(workflow): remove all .active marker file references and sync documentation

Core Changes (10 files):
- commands: cli/execute.md, memory/docs.md, workflow/review.md, workflow/brainstorm/*.md
- agents: cli-execution-agent.md
- workflows: task-core.md, workflow-architecture.md

Transformations:
- Removed all .active-* marker file operations (touch/rm/find)
- Updated session discovery to directory-based (.workflow/sessions/)
- Updated directory structure examples to show sessions/ subdirectory
- Replaced marker-based state with location-based state

Reference Documentation (57 files):
- Auto-synced via analyze_commands.py script
- Includes all core file changes
- Updated command indexes (all-commands.json, by-category.json, etc.)

Migration complete: 100% .active marker references removed
Session state now determined by directory location only

.claude/skills/command-guide/reference/agents/cli-explore-agent.md

@@ -22,7 +22,7 @@ description: |
   - Progressive disclosure: Quick overview → detailed analysis → dependency deep-dive
   - Context-aware filtering based on task requirements
 
-color: blue
+color: yellow
 ---
 
 You are a specialized **CLI Exploration Agent** that executes read-only code analysis tasks autonomously to discover module structures, map dependencies, and understand architectural patterns.
@@ -513,37 +513,19 @@ RULES: $(cat ~/.claude/workflows/cli-templates/prompts/analysis/02-analyze-code-
    - Use Gemini semantic analysis as tiebreaker
    - Document uncertainty in report with attribution
 
-## Integration with Other Agents
+## Available Tools & Services
 
-### As Service Provider (Called by Others)
-
-**Planning Agents** (`action-planning-agent`, `conceptual-planning-agent`):
-- **Use Case**: Pre-planning reconnaissance to understand existing code
-- **Input**: Task description + focus areas
-- **Output**: Structural overview + dependency analysis
-- **Flow**: Planning agent → CLI explore agent (quick-scan) → Context for planning
-
-**Execution Agents** (`code-developer`, `cli-execution-agent`):
-- **Use Case**: Refactoring impact analysis before code modifications
-- **Input**: Target files/functions to modify
-- **Output**: Dependency map + risk assessment
-- **Flow**: Execution agent → CLI explore agent (dependency-map) → Safe modification strategy
-
-**UI Design Agent** (`ui-design-agent`):
-- **Use Case**: Discover existing UI components and design tokens
-- **Input**: Component directory + file patterns
-- **Output**: Component inventory + styling patterns
-- **Flow**: UI agent delegates structure analysis to CLI explore agent
-
-### As Consumer (Calls Others)
+This agent can leverage the following tools to enhance analysis:
 
 **Context Search Agent** (`context-search-agent`):
 - **Use Case**: Get project-wide context before analysis
-- **Flow**: CLI explore agent → Context search agent → Enhanced analysis with full context
+- **When to use**: Need comprehensive project understanding beyond file structure
+- **Integration**: Call context-search-agent first, then use results to guide exploration
 
-**MCP Tools**:
+**MCP Tools** (Code Index):
 - **Use Case**: Enhanced file discovery and search capabilities
-- **Flow**: CLI explore agent → Code Index MCP → Faster pattern discovery
+- **When to use**: Large codebases requiring fast pattern discovery
+- **Integration**: Prefer Code Index MCP when available, fallback to rg/bash tools
 
 ## Key Reminders
 
@@ -636,52 +618,3 @@ rg "^import .*;" --type java -n
 # Find test files
 find . -name "*Test.java" -o -name "*Tests.java"
 ```
-
----
-
-## Performance Optimization
-
-### Caching Strategy (Optional)
-
-**Project Structure Cache**:
-- Cache `get_modules_by_depth.sh` output for 1 hour
-- Invalidate on file system changes (watch .git/index)
-
-**Pattern Match Cache**:
-- Cache rg results for common patterns (class/function definitions)
-- Invalidate on file modifications
-
-**Gemini Analysis Cache**:
-- Cache semantic analysis results for unchanged files
-- Key: file_path + content_hash
-- TTL: 24 hours
-
-### Parallel Execution
-
-**Quick-Scan Mode**:
-- Run rg searches in parallel (classes, functions, imports)
-- Merge results after completion
-
-**Deep-Scan Mode**:
-- Execute Bash scan (Phase 1) and Gemini setup concurrently
-- Wait for Phase 1 completion before Phase 2 (Gemini needs context)
-
-**Dependency-Map Mode**:
-- Discover imports and exports in parallel
-- Build graph after all discoveries complete
-
-### Resource Limits
-
-**File Count Limits**:
-- Quick-scan: Unlimited (filtered by relevance)
-- Deep-scan: Max 100 files for Gemini analysis
-- Dependency-map: Max 500 modules for graph construction
-
-**Timeout Limits**:
-- Quick-scan: 30 seconds (bash-only, fast)
-- Deep-scan: 5 minutes (includes Gemini CLI)
-- Dependency-map: 10 minutes (graph construction + analysis)
-
-**Memory Limits**:
-- Limit rg output to 10MB (use --max-count)
-- Stream large outputs instead of loading into memory