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

engine/pipeline/controller.py

@@ -111,8 +111,82 @@ class Pipeline:
                 stage.cleanup()
             except Exception:
                 pass
+
+        # Rebuild execution order and capability map if stage was removed
+        if stage and self._initialized:
+            self._rebuild()
+
         return stage
 
+    def remove_stage_safe(self, name: str, cleanup: bool = True) -> Stage | None:
+        """Remove a stage and rebuild execution order safely.
+
+        This is an alias for remove_stage() that explicitly rebuilds
+        the execution order after removal.
+
+        Args:
+            name: Name of the stage to remove
+            cleanup: If True, call cleanup() on the removed stage
+
+        Returns:
+            The removed stage, or None if not found
+        """
+        return self.remove_stage(name, cleanup)
+
+    def cleanup_stage(self, name: str) -> None:
+        """Clean up a specific stage without removing it.
+
+        This is useful for stages that need to release resources
+        (like display connections) without being removed from the pipeline.
+
+        Args:
+            name: Name of the stage to clean up
+        """
+        stage = self._stages.get(name)
+        if stage:
+            try:
+                stage.cleanup()
+            except Exception:
+                pass
+
+    def can_hot_swap(self, name: str) -> bool:
+        """Check if a stage can be safely hot-swapped.
+
+        A stage can be hot-swapped if:
+        1. It exists in the pipeline
+        2. It's not required for basic pipeline function
+        3. It doesn't have strict dependencies that can't be re-resolved
+
+        Args:
+            name: Name of the stage to check
+
+        Returns:
+            True if the stage can be hot-swapped, False otherwise
+        """
+        # Check if stage exists
+        if name not in self._stages:
+            return False
+
+        # Check if stage is a minimum capability provider
+        stage = self._stages[name]
+        stage_caps = stage.capabilities if hasattr(stage, "capabilities") else set()
+        minimum_caps = self._minimum_capabilities
+
+        # If stage provides a minimum capability, it's more critical
+        # but still potentially swappable if another stage provides the same capability
+        for cap in stage_caps:
+            if cap in minimum_caps:
+                # Check if another stage provides this capability
+                providers = self._capability_map.get(cap, [])
+                # This stage is the sole provider - might be critical
+                # but still allow hot-swap if pipeline is not initialized
+                if len(providers) <= 1 and self._initialized:
+                    return False
+
+        return True
+
+        return True
+
     def replace_stage(
         self, name: str, new_stage: Stage, preserve_state: bool = True
     ) -> Stage | None: