For existing files:

git commit -a -m "A message here"
git push

For new files

git add folder/filename
git commit -a -m "A message here"
git push

example

git add ./EloquentJavaScript/eloquentJS_1401.html
git add ./EloquentJavaScript/js/http.js

NOTE: for a reason I don't know, when my workspace was re-activated, the project from GitHub was not working properly anymore.
I could see the main folder (learning) but nothing below it. So I deleted the workspace and cloned it again. After taking these
steps it worked again.

Right click the project
Select Team and then Commit
In one of the windows which follow select the master branch and
use the option "force commit"
Then click on the button "Commit and Push"

When one repository has non-committed changes and I commit and push changes from other repositories,
(for example I don't commit from Eclipse, but I commit and push from Cloud9) then an error might happen

git  error: The following untracked working tree files would be overwritten by merge

In this case look at the file(s) in the error message and use the command

git clean -f <directory or file> 

to remove those files. After that git pull should work.

Sometimes instead of git clean I used

git rm -r <directory or file>