Source-code control Poll

I always put SoPC builder in a seperate folder.

So my tree looks something like this:

altera - Quartus project files
src - My source code, folder structure typically mirrors project hierarchy.
   |___ sopc - This is where I generate SoPC builder.
   |___ mysource1
   |___ mysource2
sim - Modelsim files
src_tb - Testbench source files
doc - documents

The way to accomplish getting SoPC builder in a folder other than the Quartus project folder is to launch it using the MegaWizard plug-in manager instead of launching directly from the "tools" menu or the SoPC builder icon on the Quartus toolbar. Using the MegaWizard plug-in manager you can specify where you want it located.

Jake