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Instead of using git add . use git add draglet-common/src/main/java/com/draglet/domain/order/LocalOrderImpl.java

Because git add . stages all the files in working directory.

You can stage individual files by using git add path/to/file1 path/to/file2

You can use git add -u path/to/file1 path/to/file2 to stage modified and deleted files.

To answer all your questions:

1. Untracked files are files that are on your file system but they are not in the list of files managed with git. If you want to track them with git you need to git-add them, otherwise to git-ignore them. In your case those are files created by your IDE and should definately be ignored
2. You should take a look here and here for the information on the .gitignore file
3. Usually that's what a git commit does. It does only wrap your modifications and then you can push them to the remote repository. However this untracked files you have are considered by git as a "contribution" and so you need to set up your repository in order to ignore them and make them not considered. Once your setup is refined properly you'll just see your desired files and you can commit 'em all. However take a look here if you need more info on the possible flags of the commit commans

Have you checked that your /etc/apt/sources.list contains lines similar to the following?