clean-up and adjustments also related with OOIION-1352 and OOIION-1495.

- capture instrument_ids associated with ports in auxiliary PortNode objects;
- for tests, always load network definition directly from yaml, not via RSN OMS (this was already done for mission manager tests, but now it's the default in the base test class)
- remove unneeded supporting class and test after these changes.

Again, changes toward resolving outstanding issue related with configuration handling using mixed mechanisms

Tests OK.

@edwardhunter please review/merge

(@bobfrat FYI minor update in test_mission_manager)