jGit - how to add all files to staging area

Question

I tried in a lot of ways to clone a repo with jGit (it works). Then, I write some archive in the repository, and tried to add all (a git add *, git add -A

Answer 1

One easy way to debug this is to look at the tests of the AddCommand in the JGit repo: AddCommandTest.java

You will see that in order to add all files the pattern "*" is never used, but "." is.
And it is used in the test function named... testAddWholeRepo()(!)

git.add().addFilepattern(".").call();

The Exception:

Exception in thread "main" org.eclipse.jgit.errors.NoWorkTreeException: 
Bare Repository has neither a working tree, nor an index

is quite explicit: you need to add file in a non-bare repo.

See test method testCloneRepository() to compare with your own clone, and see if there is any difference.