update .gitignore and remove .gitkeep files

[MarieStLaurent]

While building the repo structure, I used lots of .gitkeep files and listed many local data files under .gitignore to preserve the repo's organization without pushing a bunch of data files directly on .github.

After wrapping all those local datafiles into nested datalad datasets, update the .gitignore to track all submodule files, and remove the unecessary .gitkeep files.