I need to add the file to the repository and then commit it from my java project. I use 

Runtime.getRuntime().exec("C:\\Program Files (x86)\\Git\\bin\\sh.exe");


to start git but what should I do next?


Question: How do I add userpoints directly to the database?
Answer: Userpoints has an API.

See especially userpoints_userpointsapi() Something like this: userpoints_userpointsapi(array('uid'=&gt;$some_user, 'points'=&gt;9000));

You might also be interested in the Quiz module which supports Userpoints.