After downloading from the github you must switch to the branch you want. The "master" branch is purposefully kept empty.
On a production server, switch to MOODLE_24_STABLE branch if your site is using moodle 2.4 or 2.5.
Do NOT switch to the MOODLE_25_STABLE branch on a production server, because it has not yet been thoroughly tested. If you want to help, you are welcome to test the MOODLE_25_STABLE branch on a test server and report any bugs, remarks, etc. in this forum and in the bug tracker.
Joseph