I remember that in the past, JGit did not support symbolic links [1].

This has changed but AFAIK still depends on which version of Java and
which OS you run on. Which OS/JGit/Java do you use?

If you look into the repository that was cloned with native Git, what
exactly is /path/directory?

On the commit 5f0a7db, we have a plain folder at location1
On the master branch, the folder has been moved to location2 and a symlink was created instead at location1

If I clone the plain Git repository, the branch master is checked out and everything is fine

But If I clone it as a submodule of another repository, using JGit submodule commands, here is what happens:

JGit first clones the branch master: so in the working tree, we have a target folder at location2 and a symlink at location1

Then JGit tries to checkout the commit 5f0a7db (I don't know why or if this is normal). So, it deletes the target folder at location2. This results in a dangling link at location1. Then it tries to create the folder in location1. which results in an exception because of the dangling link as you can see from this code:



package org.eclipse.jgit.util;
...
public class FileUtils {
...
	public static void mkdirs(final File d, boolean skipExisting) throws IOException {
		if (!d.mkdirs()) {
			if (skipExisting && d.isDirectory()) return;
			throw new IOException(MessageFormat.format(JGitText.get().mkDirsFailed, d.getAbsolutePath()));
		}
	}