I\'m just entering into the wonderful world of git.
I have to submit a bunch of changes that I\'ve made on my program, located in a directory called /var/www/myapp
That's because you are versioning stuff inside /home/mylogin/gitclone and git tracks everything inside that folder. You cannot track other folders outside of this repository.
A solution might be create a submodule, or using a symbolic link using ln -s