I've always found it awkward that when I create a project the various tempo rary files the tool creates are at the top of the project tree and my files are down at the end of a branch of the subdirectory tree. This sees so up side down to me. I should be able to put all my source files in a simple d irectory in the main project folder with all the tool specific files in a s eparate directory not below and not above my folder. Then finding source a nd backing it up is a breeze.
Of course I can always put my files anywhere I want them and just point the tool to them. The tools tend to make this awkward and when the tool creat es a boilerplate file where does it want to put it? In with the other tool related files.
Then there are the various tool specific files that are still technically s ource such as the pin connection file and the timing constraints. They nee d to be with the rest of the source files too.
Not really talking about one tool. I mostly use Lattice, but I recall it i s very similar to the previous Xilinx tools and I don't recall the Altera t ools being any better in this regard either.
I guess I'm just out of step with the rest of the world. I wonder how the tools of the various Chinese startups work in this regard?