I have a directory structure like this:
.git/
.gitignore
main/
...
tools/
...
...
Inside main and tools, and any other directory, at an
[Bb]in will solve the problem, but...
Here a more extensive list of things you should ignore (sample list by GitExtension):
#ignore thumbnails created by windows
Thumbs.db
#Ignore files build by Visual Studio
*.user
*.aps
*.pch
*.vspscc
*_i.c
*_p.c
*.ncb
*.suo
*.bak
*.cache
*.ilk
*.log
[Bb]in
[Dd]ebug*/
*.sbr
obj/
[Rr]elease*/
_ReSharper*/