ef25fcaa00fc0c3da9ee6a261bf0c24f5c82eeae HEAD

try (Git git = new Git(repo)){
	git
	.checkout()
	.setName("HEAD")
	.call();
}

		RepositoryBuilder builder = new RepositoryBuilder();
		File meta = new File("/home/hb/testrepos/test/.git");
		Repository repo = builder
				.setGitDir(meta)
				.build();
		ObjectId head = repo.resolve(Constants.HEAD);
		System.err.println(head);

repo.getAllRefs()

> jgit.sh clone https://chalstrick@github.com/chalstrick/jgit.git
Cloning into 'jgit'...
2020-03-05 10:40:21 WARN  NetscapeCookieFile:266 - Configured http.cookieFile '/Users/d032780/.gitcookies' is missing
remote: Enumerating objects: 74721
Receiving objects:      100% (74721/74721)
Resolving deltas:       100% (43608/43608)
Checking out files:     100% (1875/1875)

> jgit.sh show-ref  | grep HEAD
6cd6ccb65a9952e8f6c802fa8b93026645df01dd        HEAD
> jgit.sh checkout HEAD
>

-rw-rw-r-- 1 hb hb 23 Mär  6 11:49 .git/HEAD
ref: refs/heads/master
user.name=Henning Blohm
user.email=henning.blohm@zfabrik.de
core.autocrlf=false
filesystem.Oracle Corporation|11.0.1|/dev/sdb2.timestampresolution=5000 nanoseconds
filesystem.Oracle Corporation|11.0.1|/dev/sdb2.minracythreshold=4485 microseconds
filesystem.Oracle Corporation|1.8.0_101|/dev/sdb2.timestampresolution=1002 milliseconds
filesystem.Oracle Corporation|1.8.0_101|/dev/sdb2.minracythreshold=0 nanoseconds
core.repositoryformatversion=0
core.filemode=true
core.logallrefupdates=true
remote.origin.url=/home/hb/z2-core/workspace/zzz_git_problem/source_repo
26f130cc87357f6980f500b26523730813728d51 HEAD
50b82850eb6fcad870c40cda650e6ec97aa552f8 refs/tags/tag

package zzz_git_problem;

import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.net.URISyntaxException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Comparator;

import org.eclipse.jgit.api.Git;
import org.eclipse.jgit.lib.Repository;
import org.eclipse.jgit.lib.RepositoryBuilder;
import org.eclipse.jgit.lib.StoredConfig;
import org.eclipse.jgit.transport.RemoteConfig;
import org.eclipse.jgit.transport.TagOpt;
import org.eclipse.jgit.transport.URIish;

public class FetchAndCheckout {
	private static File source = new File("source_repo");
	private static File target = new File("target_repo");
	
	public static void main(String[] args) throws Exception {
		initialize(source);
		initialize(target);
		
		// set up source repo with some commits and branches
		Git.init().setDirectory(source).call();
		try (Git git = new Git(repo(source))) {
			// add a file
			writeAndCommit(source, "first");
			git.branchCreate().setName("branch").call();
			checkout(source, "branch");
			writeAndCommit(source, "second");
			checkout(source, "master");

			// THIS BREAKS it			
//			git.tag().setName("tag").call();
		}

		
		// set up target repo with remote to source
		try (Git git = Git.init().
					setBare(false).
					setDirectory(target).
					call()) {
			
			Repository repo = git.getRepository();
			
			// add origin - clone all branches
			StoredConfig config = repo.getConfig();
			RemoteConfig remoteCfg = null;
			try {
				remoteCfg = new RemoteConfig(config, "origin");
			} catch (URISyntaxException e) {
				throw new IOException("Failed to configure origin repository", e);
			}
			remoteCfg.addURI(new URIish(source.getAbsolutePath()));
			remoteCfg.update(config);
			config.save();
		}
		
		// fetch HEAD
		try (Git git = new Git(repo(target))) {
			git.
			fetch().
			setRemote("origin").
			setRefSpecs("+HEAD:HEAD").
			setTagOpt(TagOpt.FETCH_TAGS).
			call();
		}
		
		// checkout
		try (Git git = new Git(repo(target))) {
			git
			.checkout()
			.setName("HEAD")
			.call();
		}
	}
	
	private static void initialize(File folder) throws Exception {
		Files.walk(folder.toPath())
	    .map(Path::toFile)
	    .sorted(Comparator.reverseOrder())
	    .forEach(File::delete);
	    folder.mkdirs();
    }

	private static void writeAndCommit(File root, String content) throws Exception {
		File file = new File(root,"test.txt");
		try (FileOutputStream fout = new FileOutputStream(file)) { fout.write(content.getBytes()); }
		try (Git git = new Git(repo(root))) {
			git.add().addFilepattern(file.getName()).call();
			git.commit().setMessage(content).call();
		}
	}
	
	private static void checkout(File root, String ref) throws Exception {
		try (Git git = new Git(repo(root))) {
			git.checkout().setName(ref).call();
		}
	}
	
	private static Repository repo(File root) throws Exception {
		return new RepositoryBuilder().setGitDir(new File(root,".git")).build();		
	}


}