On SVN, removing something from the filesystem directly (rather than using svn) created a load of headaches.
I haven\'t found this to be an issue when using gi
Remove files from the index, or from the working tree and the index. git rm will not remove a file from just your working directory.
Here's how you might delete a file using rm -f and then remove it from your index with git rm
$ rm -f index.html
$ git status -s
D index.html
$ git rm index.html
rm 'index.html'
$ git status -s
D index.html
However you can do this all in one go with just git rm
$ git status -s
$ git rm index.html
rm 'index.html'
$ ls
lib vendor
$ git status -s
D index.html