Hi,
I checked a few projects of mine:
- in an older project using a PLL and some on-chip memory, probably created with Quartus 14.x or 15.x, I only put the .vhd and .qip files under version control
- in a more recent project using a PLL, I only put the .qsys file under version control
- in another more-or-less recent project using gigabit-transceivers, I just gave up and put a ton of .sv, .qip, etc. files under version control
All of those projects synthesize without any problems after the non-versioned files are deleted.
So, for simple things like PLLs or memory, one or two files indeed seem enough. However, in the case of the transceiver, more files might be necessary. It is not always easy to figure out which you really need.
If in doubt, do what I did: copy the project somewhere else, delete the files you think are not needed, and synthesize. Quartus is very good at complaining when something is missing. Don't forget to try to open the IP components with the corresponding IP editor, to see if that information is also still available.
However, keep in mind that deleting files that Quartus generated means that you'll have to re-synthesize completely, which will very likely change the resource utilization and/or timing characteristics. I don't have access to fancy features like rapid recompile and logic-lock, but I assume it's not a good idea to delete synthesis artifacts if you're relying on those features.
Best regards,
GooGooCluster