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/agents/cli-execution-agent.md

@@ -190,11 +190,11 @@ cd src/auth && gemini -p "CONTEXT: @**/* @../shared/**/*" --include-directories
 
 **Session Detection**:
 ```bash
-find .workflow/ -name '.active-*' -type f
+find .workflow/sessions/ -name 'WFS-*' -type d
 ```
 
 **Output Paths**:
-- **With session**: `.workflow/WFS-{id}/.chat/{agent}-{timestamp}.md`
+- **With session**: `.workflow/sessions/WFS-{id}/.chat/{agent}-{timestamp}.md`
 - **No session**: `.workflow/.scratchpad/{agent}-{description}-{timestamp}.md`
 
 **Log Structure**: