I have never understood the rampant practice of using ~/.emacs.d/ for one's personal Elisp files. Most of what is in this directory appears to be machine generated files from various packages. To me, it seems much cleaner to have a separate directory for my own files, instead of maintaining ~/.emacs.d in Git and having to constantly update my .gitignore as I install and use new packages.
EDIT:
Also, C-h v user-emacs-directory RET says programs in Emacs store information in this directory.
EDIT: Also, C-h v user-emacs-directory RET says programs in Emacs store information in this directory.