Wherer does Quartus put files?

When you make a project, you specify a working directory. You can find that directory path along the top of your Quartus window. Your verilog or vhdl files will be in there. Files produced by Quartus will be in a folder within that directory called "output_files"

see image

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When you make a project, you specify a working directory. You can find that directory path along the top of your Quartus window. Your verilog or vhdl files will be in there. Files produced by Quartus will be in a folder within that directory called "output_files"

see image

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That is not exactly right. your hdl design can be anywhere and you point to it in project settings (add files) or in command line. I noticed if you work with tcl commands quartus appends paths in qsf but keeps old ones and so may point to old files.

It is clear where Quartus is putting the .sof and other output files. My issue is that Quartus makes two copies giving me three files. One each are located in submodules folders. That would be fine, however, when I get a compile error, I click on the error location and it opens one of the copies in a submodules folder instead of the file opened in Quartus.

Although the error description is so generic, it would appear to be a better solution to put a blinking cursor at the first stall point.

How are you adding files? and where are these files coming from? generated IP? Qsys?

I have never had a problem with files you added to a quartus project manually - it leaves them wherever they were. I also tend to generate Megawizard/IP catalog files into a known location and then add the generated files into the project manually. Then Quartus never makes a copy or messes with my file structre.