Managing Design Components

Hmmm its been a while since I've done this; I am not sure if this will satisfy all of your requirements but Quartus does have a libraries feature:

Go to Assignments -> Settings and look for "User Libraries (Current Project)" which allows you to specify directories for search as quartus goes about gathering up design files for synthesis.

There is also a global setting (for all Quartus projects) under Tools -> Options -> Global Libraries

Note that this will apply only to Quartus, and not to SOPC Builder, which still needs to be told about user-libraries of SOPC Builder components.