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Thank you very much Ted. I am not quite sure if I have to check in the folders "db" and "incremental db". Do you have any suggestions?
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The files in them are used by Quartus to speed up compilation, as they are pre-compiled versions of pieces of your design. If you don't change pieces of the design, Quartus won't repeat the compilation process of those elements and use the files in there.
I don't personally check those folders into my repository and just keep them in my local working copy. I try and keep my repo clean of most of the Quartus-generated files, otherwise the repo gets very large and slow. However, my situation is possibly unique since I am the only developer and I am the only one compiling. YMMV.
Also, sometimes I find if I get weird compilation errors (errors not relating to changes I've made, or to IP internals) I just delete those folders and do a "fresh" compile. Worked every time so far.
Hope that helps.
-Dan
EDIT: for what it's worth I am using Git/Tortoise Git to manage my version control
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