diff --git a/engine/app/main.py b/engine/app/main.py
index 183a245..53f4750 100644
--- a/engine/app/main.py
+++ b/engine/app/main.py
@@ -34,6 +34,82 @@ except ImportError:
 from .pipeline_runner import run_pipeline_mode
 
 
+def _handle_pipeline_mutation(pipeline: Pipeline, command: dict) -> bool:
+    """Handle pipeline mutation commands from REPL or other external control.
+
+    Args:
+        pipeline: The pipeline to mutate
+        command: Command dictionary with 'action' and other parameters
+
+    Returns:
+        True if command was successfully handled, False otherwise
+    """
+    action = command.get("action")
+
+    if action == "add_stage":
+        print(f"  [Pipeline] add_stage command received: {command}")
+        return True
+
+    elif action == "remove_stage":
+        stage_name = command.get("stage")
+        if stage_name:
+            result = pipeline.remove_stage(stage_name)
+            print(f"  [Pipeline] Removed stage '{stage_name}': {result is not None}")
+            return result is not None
+
+    elif action == "replace_stage":
+        stage_name = command.get("stage")
+        print(f"  [Pipeline] replace_stage command received: {command}")
+        return True
+
+    elif action == "swap_stages":
+        stage1 = command.get("stage1")
+        stage2 = command.get("stage2")
+        if stage1 and stage2:
+            result = pipeline.swap_stages(stage1, stage2)
+            print(f"  [Pipeline] Swapped stages '{stage1}' and '{stage2}': {result}")
+            return result
+
+    elif action == "move_stage":
+        stage_name = command.get("stage")
+        after = command.get("after")
+        before = command.get("before")
+        if stage_name:
+            result = pipeline.move_stage(stage_name, after, before)
+            print(f"  [Pipeline] Moved stage '{stage_name}': {result}")
+            return result
+
+    elif action == "enable_stage":
+        stage_name = command.get("stage")
+        if stage_name:
+            result = pipeline.enable_stage(stage_name)
+            print(f"  [Pipeline] Enabled stage '{stage_name}': {result}")
+            return result
+
+    elif action == "disable_stage":
+        stage_name = command.get("stage")
+        if stage_name:
+            result = pipeline.disable_stage(stage_name)
+            print(f"  [Pipeline] Disabled stage '{stage_name}': {result}")
+            return result
+
+    elif action == "cleanup_stage":
+        stage_name = command.get("stage")
+        if stage_name:
+            pipeline.cleanup_stage(stage_name)
+            print(f"  [Pipeline] Cleaned up stage '{stage_name}'")
+            return True
+
+    elif action == "can_hot_swap":
+        stage_name = command.get("stage")
+        if stage_name:
+            can_swap = pipeline.can_hot_swap(stage_name)
+            print(f"  [Pipeline] Can hot-swap '{stage_name}': {can_swap}")
+            return True
+
+    return False
+
+
 def main():
     """Main entry point - all modes now use presets or CLI construction."""
     if config.PIPELINE_DIAGRAM:
@@ -391,6 +467,20 @@ def run_pipeline_mode_direct():
                     except Exception:
                         pass
 
+    # Check for REPL effect in pipeline
+    repl_effect = None
+    for stage in pipeline.stages.values():
+        if isinstance(stage, EffectPluginStage) and stage._effect.name == "repl":
+            repl_effect = stage._effect
+            print(
+                "  \033[38;5;46mREPL effect detected - Interactive mode enabled\033[0m"
+            )
+            break
+
+    # Enable raw mode for REPL if present and not already enabled
+    if repl_effect and hasattr(display, "set_raw_mode"):
+        display.set_raw_mode(True)
+
     # Run pipeline loop
     from engine.display import render_ui_panel
 
@@ -453,6 +543,31 @@ def run_pipeline_mode_direct():
                     except Exception:
                         pass
 
+            # --- REPL Input Handling ---
+            if repl_effect and hasattr(display, "get_input_keys"):
+                # Get keyboard input (non-blocking)
+                keys = display.get_input_keys(timeout=0.0)
+
+                for key in keys:
+                    if key == "return":
+                        # Get command string before processing
+                        cmd_str = repl_effect.state.current_command
+                        if cmd_str:
+                            repl_effect.process_command(cmd_str, ctx)
+                            # Check for pending pipeline mutations
+                            pending = repl_effect.get_pending_command()
+                            if pending:
+                                _handle_pipeline_mutation(pipeline, pending)
+                    elif key == "up":
+                        repl_effect.navigate_history(-1)
+                    elif key == "down":
+                        repl_effect.navigate_history(1)
+                    elif key == "backspace":
+                        repl_effect.backspace()
+                    elif len(key) == 1:
+                        repl_effect.append_to_command(key)
+            # --- End REPL Input Handling ---
+
             # Check for quit request
             if hasattr(display, "is_quit_requested") and display.is_quit_requested():
                 if hasattr(display, "clear_quit_request"):