Swap System/Universe Parsing from Folders to only universe.ini referenced systems and bases

[IrateRedKite]

When scanning a modded install where universe.ini, system and base files have been moved, it becomes clear that rather than reading universe.ini to locate the base files, the application simply parses every file in the hardcoded data/universe/systems directory. Obviously this generates a ton of issues as these files are not hardcoded or referenced by the mod at all.

The parser needs to be changed to purely look at things that are referenced via ini, and not using folders unless paths are hardcoded (The MISSION folder is a good example of this)