Personally, to keep my documents like Inkscape files or LibreOffice documents separate from my code, I add a directory under my home directory called Development. There, I can do git clones to my heart's content
They are the project's subfolders (outside of the Git repo):
code contains the source code; version-controlled with Git.
wiki contains documentation and also version-controlled.
designs contains GIMP, Inkscape or Krita save files.
This structure works for me since software projects involve more things than just the code, and you can add more subfolders according to your liking such as notes, pkgbuild (for Arch Linux), or releases.
Ah, interesting. In my current setup, I dump the auxilliary files into a folder above the repo, but it can certainly make it a bit messy to find the repo in there then...
I maintain a rule that all files above the repo must be inside a folder, with one exception: a README file. Including the code folder, this typically results in no more than 5 folders; the project folder itself is kept organized and uncluttered.