Git is saying everything is up to date but there is a file missing on one node's copy of the source tree. On system A:
$ ls -l
abc.py
xyz.py
$ git add xyz.py
$ git status
nothing added to commit...
$ git commit
nothing added to commit...
$ git push
Everything up-to-date
On system B:
$ git pull
Already up-to-date
$ ls -l
abc.py
My question is: What happened to file xyz.py on system B? Why did the pull not create it on System B?