[BUG] Hybrid discovery merge pipeline does not suppress runtime entities linked to manifest entities

[bburda]

Bug report

Steps to reproduce

1. Configure gateway in hybrid mode with a manifest that defines entities with hyphenated IDs (e.g., lidar-sim, fault-manager)
2. Ensure create_synthetic_components: false in config (though the bug occurs regardless of this setting)
3. Start the gateway with ROS 2 nodes whose names match manifest ros_binding entries
4. Query entity collection endpoints (GET /areas, /components, /apps)

Reproducible with any selfpatch_demos demo (sensor_diagnostics, moveit_pick_place, turtlebot3_integration).

Expected behavior

After runtime linking matches runtime nodes to manifest entities via ros_binding, the merge pipeline should emit only the manifest-defined entities. Linked runtime entities should be suppressed/merged into their manifest counterparts.

For sensor_diagnostics demo:

• Areas: 4 (sensors, processing, diagnostics, bridge)
• Components: 8 (lidar-unit, imu-unit, gps-unit, camera-unit, compute-unit, gateway, fault-manager, diagnostic-bridge-unit)
• Apps: 8 (lidar-sim, imu-sim, gps-sim, camera-sim, anomaly-detector, medkit-gateway, medkit-fault-manager, diagnostic-bridge)

Actual behavior

Both manifest entities AND linked runtime entities appear in API responses, creating duplicates:

Areas: 6 instead of 4

sensors, processing, diagnostics, bridge, fault_manager, root

Extra: fault_manager (synthetic area from runtime), root (synthetic area)

Components: 17 instead of 8

lidar-unit, imu-unit, gps-unit, camera-unit, compute-unit, gateway, fault-manager, diagnostic-bridge-unit,
lidar_sim, camera_sim, imu_sim, gps_sim, anomaly_detector, diagnostic_bridge, ros2_medkit_gateway, _param_client_node, fault_manager

The bottom 9 are runtime-created synthetic entities with underscored IDs that should have been merged.

Apps: 17 instead of 8
Same pattern - every manifest app has a corresponding unmerged runtime duplicate.

Gateway logs show linking succeeds but duplicates still appear:

Runtime linking: 8 linked, 9 unlinked, 1 orphan nodes
MergePipeline: 43 entities from 4 layers, 4 enriched, 0 conflicts

The merge pipeline likely compares entity IDs directly (underscored != hyphenated) instead of using the ros_binding linkage to identify duplicates.

Environment

• ros2_medkit version: main (v0.4.0)
• ROS 2 distro: Jazzy
• OS: Ubuntu 24.04 (Docker)

Additional information

• create_synthetic_components: false does not prevent this - it only changes the grouping strategy, not whether runtime entities are created
• The graph_provider plugin is NOT the source of duplicates - it only enriches existing entities, does not create new ones
• Discovered while adding entity count assertions to selfpatch_demos smoke tests (test: extend smoke tests for v0.4.0 features and missing API coverage selfpatch_demos#53)