feat: Complete Pipeline Mutation API implementation

- Add can_hot_swap() function to Pipeline class
- Add cleanup_stage() method to Pipeline class
- Fix remove_stage() to rebuild execution order after removal
- Extend ui_panel.execute_command() with docstrings for mutation commands
- Update WebSocket handler to support pipeline mutation commands
- Add _handle_pipeline_mutation() function for command routing
- Add comprehensive integration tests in test_pipeline_mutation_commands.py
- Update AGENTS.md with mutation API documentation

Issue: #35 (Pipeline Mutation API)
Acceptance criteria met:
- ✅ can_hot_swap() checker for stage compatibility
- ✅ cleanup_stage() cleans up specific stages
- ✅ remove_stage_safe() rebuilds execution order (via remove_stage)
- ✅ Unit tests for all operations
- ✅ Integration with WebSocket commands
- ✅ Documentation in AGENTS.md

AGENTS.md

@@ -362,6 +362,43 @@ The rendering pipeline is documented in `docs/PIPELINE.md` using Mermaid diagram
 2. If adding new SVG diagrams, render them manually using an external tool (e.g., Mermaid Live Editor)
 3. Commit both the markdown and any new diagram files
 
+### Pipeline Mutation API
+
+The Pipeline class supports dynamic mutation during runtime via the mutation API:
+
+**Core Methods:**
+- `add_stage(name, stage, initialize=True)` - Add a stage to the pipeline
+- `remove_stage(name, cleanup=True)` - Remove a stage and rebuild execution order
+- `replace_stage(name, new_stage, preserve_state=True)` - Replace a stage with another
+- `swap_stages(name1, name2)` - Swap two stages
+- `move_stage(name, after=None, before=None)` - Move a stage in execution order
+- `enable_stage(name)` - Enable a stage
+- `disable_stage(name)` - Disable a stage
+
+**New Methods (Issue #35):**
+- `cleanup_stage(name)` - Clean up specific stage without removing it
+- `remove_stage_safe(name, cleanup=True)` - Alias for remove_stage that explicitly rebuilds
+- `can_hot_swap(name)` - Check if a stage can be safely hot-swapped
+  - Returns False for stages that provide minimum capabilities as sole provider
+  - Returns True for swappable stages
+
+**WebSocket Commands:**
+Commands can be sent via WebSocket to mutate the pipeline at runtime:
+```json
+{"action": "remove_stage", "stage": "stage_name"}
+{"action": "swap_stages", "stage1": "name1", "stage2": "name2"}
+{"action": "enable_stage", "stage": "stage_name"}
+{"action": "disable_stage", "stage": "stage_name"}
+{"action": "cleanup_stage", "stage": "stage_name"}
+{"action": "can_hot_swap", "stage": "stage_name"}
+```
+
+**Implementation Files:**
+- `engine/pipeline/controller.py` - Pipeline class with mutation methods
+- `engine/app/pipeline_runner.py` - `_handle_pipeline_mutation()` function
+- `engine/pipeline/ui.py` - execute_command() with docstrings
+- `tests/test_pipeline_mutation_commands.py` - Integration tests
+
 ## Skills Library
 
 A skills library MCP server (`skills`) is available for capturing and tracking learned knowledge. Skills are stored in `~/.skills/`.