Forcing a github push after major changes

[zivoni]

It seems that you have your files untracked, so you need to add files first, after that you can commit them into the repository.  Try 

Output:
git add .
git commit

in your directory before pushing.

EDIT: I have overlooked your other questions. I am not a big git expert, but from my understanding if you move or rename files/directories, from git's point of view they disappeared (so git status lists them as deleted), while renamed/moved files are untracked by git and you need to add your changes with git add . . After that you can commit and push your changes.

Git has no problems with binary files, actually it doesnt care at all - even for text files git just computes sha-1 for files and if it changes, git saves entire file (in his internal compressed format). So you can put your binary into the repository and add and commit.