org.eclipse.jgit.api.errors.JGitInternalException: Exception caught during execution of merge command. org.eclipse.
jgit.errors.MissingObjectException: Missing commit d8cce2103d8e36d0d924d93f1ac6b882c10b9a20
        at org.eclipse.jgit.api.MergeCommand.call(MergeCommand.java:220)
        at org.eclipse.jgit.api.PullCommand.call(PullCommand.java:255)

$ git status
fatal: bad object HEAD

$ git read-tree HEAD
fatal: failed to unpack tree object HEAD

$ git pull
error: refs/heads/master does not point to a valid object!
error: refs/remotes/origin/master does not point to a valid object!
error: refs/heads/master does not point to a valid object!
error: refs/remotes/origin/master does not point to a valid object!
error: refs/heads/master does not point to a valid object!
error: refs/remotes/origin/master does not point to a valid object!
error: refs/heads/master does not point to a valid object!
error: refs/remotes/origin/master does not point to a valid object!
remote: Counting objects: 1684, done.
remote: Compressing objects: 100% (1128/1128), done.
remote: Total 1684 (delta 452), reused 1453 (delta 376)
Receiving objects: 100% (1684/1684), 232.59 KiB, done.
Resolving deltas: 100% (452/452), done.
From localhost:/test
 * [new branch]      master     -> origin/master
Already up-to-date.

$ git status
# On branch master
nothing to commit (working directory clean)

git.pull().call();

    public boolean refresh()  {
        boolean status = false;
        try {
            git.pull().call();
            status = true;
        }
        catch (JGitInternalException e) {
            if (e.getCause() instanceof MissingObjectException) {
                log.error("JGit Error occurred, trying to recover with Native Git");
                // Lets attempt and recover using Native Git. Something went
                // wrong using JGit Merge.
                status = nativeRefresh();
            } else {
                log.error("JGit Error recovery failed. " + e.getMessage(), e);
            }
        }
        catch (GitAPIException e) {
            log.error("Cannot find Git repository. " + e.getMessage(), e);
        }
        return status;
    }


    private boolean nativeRefresh() {
        boolean status = false;
        String[] commandLine = new String[] {
                "c:/Git/bin/sh.exe",
                "--login",
                "-i",
                "-c",
                "git pull"
        };
        ProcessBuilder pb = new ProcessBuilder(commandLine);
        pb.directory(new File("C:/repo/"));
        pb.redirectErrorStream(true);
        try {
            Process p = pb.start();
            status = p.waitFor() == 0 ? true : false;
            p.destroy();
        } catch (IOException e) {
            log.error("Git pull process cannot successfully start. ", e);
        } catch (InterruptedException e) {
            log.error("Something went wrong waiting for Git pull to complete", e);
        }
        return status;
    }