I don't know if this request falls into the goals of HaystackContinued, but did you considered at some point to add custom filters or even "folders" for different vessels?
E.g. I have a fleet of probes for long distance communication (remotetech mod) and i'd like to keep them all under the same directory. Is it possible to do this with HaystackContinued? If no would you consider to add this feature or maybe a pull request for it?
Current release (v0.4.0.0) causes an exception at start:
IsolatedStorageException: Could not find file "C:\Program Files (x86)\Steam\steamapps\common\Kerbal Space Program\GameData\HaystackContinued\icons\button_vessel_spaceobject.png".
The settings.cfg file of HaystackContinued stores volatile data. ModuleManager vacuums settings.cfg files into its config cache, which is completely unnecessary because the cache is meant for constant configs. Any change to this file forces ModuleManager to rebuild its cache on each game start. If you move the path for the settings.cfg to the /HaystackContinued/PluginData MM will avoid caching that folder, this will speed up the game loading time for all the users.