Don't prune symbolic refs when fetch.prune = true The canonical implementation also doesn't. Compare current code in remote.c, function get_stale_heads_cb.[1] Not handling symrefs in this case was introduced in canonical git in [2] in 2008. [1] https://github.com/git/git/blob/v2.17.0/remote.c#L2259 [2] https://github.com/git/git/commit/740fdd27f0 Bug: 533549 Change-Id: If348d56bb4a96b8aa7141f7e7b5a0d3dd4e7808b Signed-off-by: Thomas Wolf <thomas.wolf@paranor.ch>

diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/FetchCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/FetchCommandTest.java
index cf1afce..4c2c0e8 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/FetchCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/FetchCommandTest.java

@@ -43,10 +43,15 @@
 package org.eclipse.jgit.api;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
 
+import java.io.File;
 import java.util.Collection;
 
+import org.eclipse.jgit.junit.JGitTestUtil;
 import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
@@ -204,4 +209,43 @@ public void fetchWithExplicitTagsShouldUpdateLocal() throws Exception {
 		assertEquals(RefUpdate.Result.FORCED, update.getResult());
 		assertEquals(tagRef2.getObjectId(), db.resolve(tagName));
 	}
+
+	@Test
+	public void testFetchWithPruneShouldKeepOriginHead() throws Exception {
+		// Create a commit in the test repo.
+		commitFile("foo", "foo", "master");
+		// Produce a real clone of the git repo
+		Git cloned = Git.cloneRepository()
+				.setDirectory(createTempDirectory("testCloneRepository"))
+				.setURI("file://"
+						+ git.getRepository().getWorkTree().getAbsolutePath())
+				.call();
+		assertNotNull(cloned);
+		Repository clonedRepo = cloned.getRepository();
+		addRepoToClose(clonedRepo);
+		ObjectId originMasterId = clonedRepo
+				.resolve("refs/remotes/origin/master");
+		assertNotNull("Should have origin/master", originMasterId);
+		assertNotEquals("origin/master should not be zero ID",
+				ObjectId.zeroId(), originMasterId);
+		// Canonical git creates origin/HEAD; JGit (for now) doesn't. Let's
+		// pretend we did the clone via command-line git.
+		ObjectId originHeadId = clonedRepo.resolve("refs/remotes/origin/HEAD");
+		if (originHeadId == null) {
+			JGitTestUtil.write(
+					new File(clonedRepo.getDirectory(),
+							"refs/remotes/origin/HEAD"),
+					"ref: refs/remotes/origin/master\n");
+			originHeadId = clonedRepo.resolve("refs/remotes/origin/HEAD");
+		}
+		assertEquals("Should have origin/HEAD", originMasterId, originHeadId);
+		FetchResult result = cloned.fetch().setRemote("origin")
+				.setRemoveDeletedRefs(true).call();
+		assertTrue("Fetch after clone should be up-to-date",
+				result.getTrackingRefUpdates().isEmpty());
+		assertEquals("origin/master should still exist", originMasterId,
+				clonedRepo.resolve("refs/remotes/origin/master"));
+		assertEquals("origin/HEAD should be unchanged", originHeadId,
+				clonedRepo.resolve("refs/remotes/origin/HEAD"));
+	}
 }

diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
index 51f900b..ff183c8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java

@@ -480,6 +480,9 @@ private Map<String, Ref> localRefs() throws TransportException {
 	private void deleteStaleTrackingRefs(FetchResult result,
 			BatchRefUpdate batch) throws IOException {
 		for (Ref ref : localRefs().values()) {
+			if (ref.isSymbolic()) {
+				continue;
+			}
 			final String refname = ref.getName();
 			for (RefSpec spec : toFetch) {
 				if (spec.matchDestination(refname)) {