Merge branch 'stable-4.11' into stable-5.0

* stable-4.11:
  Silence API warning for new ObjectIdSerializer introduced in 4.11.1
  Ignore API warnings
  Fix photon target platform to use photon version of org.eclipse.osgi
  Update Photon orbit repository to R20180606145124
  Suppress warning for trying to delete non-empty directory
  Fix fetching with duplicate ref updates
  Fetch(Process): should tolerate duplicate refspecs
  FetchCommandTest: test add/update/delete fetch

Change-Id: I2497f99b7d0686a0e0f773c39c8725e813ce9d4a
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

org.eclipse.jgit.http.apache/.settings/.api_filters

@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<component id="org.eclipse.jgit.http.apache" version="2">
-    <resource path="META-INF/MANIFEST.MF">
-        <filter id="925892614">
-            <message_arguments>
-                <message_argument value="5.0.0"/>
-                <message_argument value="4.11.0"/>
-            </message_arguments>
-        </filter>
-    </resource>
-</component>

org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.5.target

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/mbarbero/fr.obeo.releng.targetplatform -->
-<target name="jgit-4.5" sequenceNumber="1528375371">
+<target name="jgit-4.5" sequenceNumber="1535179254">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.4.8.v20171121"/>

org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.target

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/mbarbero/fr.obeo.releng.targetplatform -->
-<target name="jgit-4.6" sequenceNumber="1528375359">
+<target name="jgit-4.6" sequenceNumber="1535179241">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.4.8.v20171121"/>

org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.7.target

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/mbarbero/fr.obeo.releng.targetplatform -->
-<target name="jgit-4.7" sequenceNumber="1528375339">
+<target name="jgit-4.7" sequenceNumber="1535179221">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.4.8.v20171121"/>

org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.8.target

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/mbarbero/fr.obeo.releng.targetplatform -->
-<target name="jgit-4.8" sequenceNumber="1528872727">
+<target name="jgit-4.8" sequenceNumber="1535179205">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.4.8.v20171121"/>
@@ -33,6 +33,8 @@
       <unit id="org.apache.commons.logging.source" version="1.1.1.v201101211721"/>
       <unit id="org.apache.httpcomponents.httpcore" version="4.4.6.v20170210-0925"/>
       <unit id="org.apache.httpcomponents.httpcore.source" version="4.4.6.v20170210-0925"/>
+      <unit id="org.apache.httpcomponents.httpclient" version="4.5.2.v20180410-1551"/>
+      <unit id="org.apache.httpcomponents.httpclient.source" version="4.5.2.v20180410-1551"/>
       <unit id="org.apache.log4j" version="1.2.15.v201012070815"/>
       <unit id="org.apache.log4j.source" version="1.2.15.v201012070815"/>
       <unit id="org.kohsuke.args4j" version="2.33.0.v20160323-2218"/>
@@ -66,14 +68,9 @@
       <unit id="com.jcraft.jzlib.source" version="1.1.1.v201205102305"/>
       <repository location="http://download.eclipse.org/tools/orbit/downloads/drops/R20180606145124/repository"/>
     </location>
-    <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
-      <unit id="org.apache.httpcomponents.httpclient" version="4.5.2.v20170210-0925"/>
-      <unit id="org.apache.httpcomponents.httpclient.source" version="4.5.2.v20170210-0925"/>
-      <repository location="http://download.eclipse.org/tools/orbit/downloads/drops/R20170919201930/repository/"/>
-    </location>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.osgi" version="0.0.0"/>
-      <repository location="http://download.eclipse.org/releases/oxygen/"/>
+      <repository location="http://download.eclipse.org/releases/photon/"/>
     </location>
   </locations>
 </target>

org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.8.tpd

@@ -3,6 +3,6 @@ target "jgit-4.8" with source configurePhase
 include "projects/jetty-9.4.8.tpd"
 include "orbit/R20180606145124-Photon.tpd"
 
-location "http://download.eclipse.org/releases/oxygen/" {
+location "http://download.eclipse.org/releases/photon/" {
 	org.eclipse.osgi lazy
 }

org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20180606145124-Photon.tpd

@@ -12,6 +12,8 @@ location "http://download.eclipse.org/tools/orbit/downloads/drops/R2018060614512
 	org.apache.commons.logging.source [1.1.1.v201101211721,1.1.1.v201101211721]
 	org.apache.httpcomponents.httpcore [4.4.6.v20170210-0925,4.4.6.v20170210-0925]
 	org.apache.httpcomponents.httpcore.source [4.4.6.v20170210-0925,4.4.6.v20170210-0925]
+	org.apache.httpcomponents.httpclient [4.5.2.v20180410-1551,4.5.2.v20180410-1551]
+	org.apache.httpcomponents.httpclient.source [4.5.2.v20180410-1551,4.5.2.v20180410-1551]
 	org.apache.log4j [1.2.15.v201012070815,1.2.15.v201012070815]
 	org.apache.log4j.source [1.2.15.v201012070815,1.2.15.v201012070815]
 	org.kohsuke.args4j [2.33.0.v20160323-2218,2.33.0.v20160323-2218]
@@ -44,9 +46,3 @@ location "http://download.eclipse.org/tools/orbit/downloads/drops/R2018060614512
 	com.jcraft.jzlib [1.1.1.v201205102305,1.1.1.v201205102305]
 	com.jcraft.jzlib.source [1.1.1.v201205102305,1.1.1.v201205102305]
 }
-
-location "http://download.eclipse.org/tools/orbit/downloads/drops/R20170919201930/repository/" {
-	// platform uses this outdated version of httpclient in Photon
-	org.apache.httpcomponents.httpclient [4.5.2.v20170210-0925,4.5.2.v20170210-0925]
-	org.apache.httpcomponents.httpclient.source [4.5.2.v20170210-0925,4.5.2.v20170210-0925]
-}

org.eclipse.jgit.pgm/.settings/.api_filters

@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<component id="org.eclipse.jgit.pgm" version="2">
-    <resource path="META-INF/MANIFEST.MF">
-        <filter id="925892614">
-            <message_arguments>
-                <message_argument value="5.0.0"/>
-                <message_argument value="4.11.0"/>
-            </message_arguments>
-        </filter>
-    </resource>
-</component>

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/FetchCommandTest.java

@@ -49,7 +49,9 @@ import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
 
 import java.io.File;
+import java.util.ArrayList;
 import java.util.Collection;
+import java.util.List;
 
 import org.eclipse.jgit.junit.JGitTestUtil;
 import org.eclipse.jgit.junit.RepositoryTestCase;
@@ -61,6 +63,7 @@ import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.transport.FetchResult;
+import org.eclipse.jgit.transport.RefSpec;
 import org.eclipse.jgit.transport.RemoteConfig;
 import org.eclipse.jgit.transport.TagOpt;
 import org.eclipse.jgit.transport.TrackingRefUpdate;
@@ -125,6 +128,91 @@ public class FetchCommandTest extends RepositoryTestCase {
 				res.getTrackingRefUpdate("refs/heads/master").getResult());
 	}
 
+	@Test
+	public void fetchAddsBranches() throws Exception {
+		final String branch1 = "b1";
+		final String branch2 = "b2";
+		final String remoteBranch1 = "test/" + branch1;
+		final String remoteBranch2 = "test/" + branch2;
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef1 = remoteGit.branchCreate().setName(branch1).call();
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef2 = remoteGit.branchCreate().setName(branch2).call();
+
+		String spec = "refs/heads/*:refs/remotes/test/*";
+		git.fetch().setRemote("test").setRefSpecs(spec).call();
+		assertEquals(branchRef1.getObjectId(), db.resolve(remoteBranch1));
+		assertEquals(branchRef2.getObjectId(), db.resolve(remoteBranch2));
+	}
+
+	@Test
+	public void fetchDoesntDeleteBranches() throws Exception {
+		final String branch1 = "b1";
+		final String branch2 = "b2";
+		final String remoteBranch1 = "test/" + branch1;
+		final String remoteBranch2 = "test/" + branch2;
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef1 = remoteGit.branchCreate().setName(branch1).call();
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef2 = remoteGit.branchCreate().setName(branch2).call();
+
+		String spec = "refs/heads/*:refs/remotes/test/*";
+		git.fetch().setRemote("test").setRefSpecs(spec).call();
+		assertEquals(branchRef1.getObjectId(), db.resolve(remoteBranch1));
+		assertEquals(branchRef2.getObjectId(), db.resolve(remoteBranch2));
+
+		remoteGit.branchDelete().setBranchNames(branch1).call();
+		git.fetch().setRemote("test").setRefSpecs(spec).call();
+		assertEquals(branchRef1.getObjectId(), db.resolve(remoteBranch1));
+		assertEquals(branchRef2.getObjectId(), db.resolve(remoteBranch2));
+	}
+
+	@Test
+	public void fetchUpdatesBranches() throws Exception {
+		final String branch1 = "b1";
+		final String branch2 = "b2";
+		final String remoteBranch1 = "test/" + branch1;
+		final String remoteBranch2 = "test/" + branch2;
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef1 = remoteGit.branchCreate().setName(branch1).call();
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef2 = remoteGit.branchCreate().setName(branch2).call();
+
+		String spec = "refs/heads/*:refs/remotes/test/*";
+		git.fetch().setRemote("test").setRefSpecs(spec).call();
+		assertEquals(branchRef1.getObjectId(), db.resolve(remoteBranch1));
+		assertEquals(branchRef2.getObjectId(), db.resolve(remoteBranch2));
+
+		remoteGit.commit().setMessage("commit").call();
+		branchRef2 = remoteGit.branchCreate().setName(branch2).setForce(true).call();
+		git.fetch().setRemote("test").setRefSpecs(spec).call();
+		assertEquals(branchRef1.getObjectId(), db.resolve(remoteBranch1));
+		assertEquals(branchRef2.getObjectId(), db.resolve(remoteBranch2));
+	}
+
+	@Test
+	public void fetchPrunesBranches() throws Exception {
+		final String branch1 = "b1";
+		final String branch2 = "b2";
+		final String remoteBranch1 = "test/" + branch1;
+		final String remoteBranch2 = "test/" + branch2;
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef1 = remoteGit.branchCreate().setName(branch1).call();
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef2 = remoteGit.branchCreate().setName(branch2).call();
+
+		String spec = "refs/heads/*:refs/remotes/test/*";
+		git.fetch().setRemote("test").setRefSpecs(spec).call();
+		assertEquals(branchRef1.getObjectId(), db.resolve(remoteBranch1));
+		assertEquals(branchRef2.getObjectId(), db.resolve(remoteBranch2));
+
+		remoteGit.branchDelete().setBranchNames(branch1).call();
+		git.fetch().setRemote("test").setRefSpecs(spec)
+				.setRemoveDeletedRefs(true).call();
+		assertNull(db.resolve(remoteBranch1));
+		assertEquals(branchRef2.getObjectId(), db.resolve(remoteBranch2));
+	}
+
 	@Test
 	public void fetchShouldAutoFollowTag() throws Exception {
 		remoteGit.commit().setMessage("commit").call();
@@ -248,4 +336,75 @@ public class FetchCommandTest extends RepositoryTestCase {
 		assertEquals("origin/HEAD should be unchanged", originHeadId,
 				clonedRepo.resolve("refs/remotes/origin/HEAD"));
 	}
+
+	@Test
+	public void fetchAddRefsWithDuplicateRefspec() throws Exception {
+		final String branchName = "branch";
+		final String remoteBranchName = "test/" + branchName;
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef = remoteGit.branchCreate().setName(branchName).call();
+
+		final String spec1 = "+refs/heads/*:refs/remotes/test/*";
+		final String spec2 = "refs/heads/*:refs/remotes/test/*";
+		final StoredConfig config = db.getConfig();
+		RemoteConfig remoteConfig = new RemoteConfig(config, "test");
+		remoteConfig.addFetchRefSpec(new RefSpec(spec1));
+		remoteConfig.addFetchRefSpec(new RefSpec(spec2));
+		remoteConfig.update(config);
+
+		git.fetch().setRemote("test").setRefSpecs(spec1).call();
+		assertEquals(branchRef.getObjectId(), db.resolve(remoteBranchName));
+	}
+
+	@Test
+	public void fetchPruneRefsWithDuplicateRefspec()
+			throws Exception {
+		final String branchName = "branch";
+		final String remoteBranchName = "test/" + branchName;
+		remoteGit.commit().setMessage("commit").call();
+		Ref branchRef = remoteGit.branchCreate().setName(branchName).call();
+
+		final String spec1 = "+refs/heads/*:refs/remotes/test/*";
+		final String spec2 = "refs/heads/*:refs/remotes/test/*";
+		final StoredConfig config = db.getConfig();
+		RemoteConfig remoteConfig = new RemoteConfig(config, "test");
+		remoteConfig.addFetchRefSpec(new RefSpec(spec1));
+		remoteConfig.addFetchRefSpec(new RefSpec(spec2));
+		remoteConfig.update(config);
+
+		git.fetch().setRemote("test").setRefSpecs(spec1).call();
+		assertEquals(branchRef.getObjectId(), db.resolve(remoteBranchName));
+
+		remoteGit.branchDelete().setBranchNames(branchName).call();
+		git.fetch().setRemote("test").setRefSpecs(spec1)
+				.setRemoveDeletedRefs(true).call();
+		assertNull(db.resolve(remoteBranchName));
+	}
+
+	@Test
+	public void fetchUpdateRefsWithDuplicateRefspec() throws Exception {
+		final String tagName = "foo";
+		remoteGit.commit().setMessage("commit").call();
+		Ref tagRef1 = remoteGit.tag().setName(tagName).call();
+		List<RefSpec> refSpecs = new ArrayList<>();
+		refSpecs.add(new RefSpec("+refs/heads/*:refs/remotes/origin/*"));
+		refSpecs.add(new RefSpec("+refs/tags/*:refs/tags/*"));
+		// Updating tags via the RefSpecs and setting TagOpt.FETCH_TAGS (or
+		// AUTO_FOLLOW) will result internally in *two* updates for the same
+		// ref.
+		git.fetch().setRemote("test").setRefSpecs(refSpecs)
+				.setTagOpt(TagOpt.AUTO_FOLLOW).call();
+		assertEquals(tagRef1.getObjectId(), db.resolve(tagName));
+
+		remoteGit.commit().setMessage("commit 2").call();
+		Ref tagRef2 = remoteGit.tag().setName(tagName).setForceUpdate(true)
+				.call();
+		FetchResult result = git.fetch().setRemote("test").setRefSpecs(refSpecs)
+				.setTagOpt(TagOpt.FETCH_TAGS).call();
+		assertEquals(2, result.getTrackingRefUpdates().size());
+		TrackingRefUpdate update = result
+				.getTrackingRefUpdate(Constants.R_TAGS + tagName);
+		assertEquals(RefUpdate.Result.FORCED, update.getResult());
+		assertEquals(tagRef2.getObjectId(), db.resolve(tagName));
+	}
 }

org.eclipse.jgit.ui/.settings/.api_filters

@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<component id="org.eclipse.jgit.ui" version="2">
-    <resource path="META-INF/MANIFEST.MF">
-        <filter id="925892614">
-            <message_arguments>
-                <message_argument value="5.0.0"/>
-                <message_argument value="4.11.0"/>
-            </message_arguments>
-        </filter>
-    </resource>
-</component>

org.eclipse.jgit/.settings/.api_filters

@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<component id="org.eclipse.jgit" version="2">
-    <resource path="src/org/eclipse/jgit/lib/ObjectIdSerializer.java" type="org.eclipse.jgit.lib.ObjectIdSerializer">
-        <filter id="1141899266">
-            <message_arguments>
-                <message_argument value="4.11"/>
-                <message_argument value="5.0"/>
-                <message_argument value="readWithoutMarker(InputStream)"/>
-            </message_arguments>
-        </filter>
-        <filter id="1141899266">
-            <message_arguments>
-                <message_argument value="4.11"/>
-                <message_argument value="5.0"/>
-                <message_argument value="writeWithoutMarker(OutputStream, AnyObjectId)"/>
-            </message_arguments>
-        </filter>
-    </resource>
-</component>

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java

@@ -65,6 +65,7 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.InterruptedIOException;
+import java.nio.file.DirectoryNotEmptyException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.security.DigestInputStream;
@@ -1287,6 +1288,10 @@ public class RefDirectory extends RefDatabase {
 		for (int i = 0; i < depth; ++i) {
 			try {
 				Files.delete(dir.toPath());
+			} catch (DirectoryNotEmptyException e) {
+				// Don't log; normal case when there are other refs with the
+				// same prefix
+				break;
 			} catch (IOException e) {
 				LOG.warn("Unable to remove path {}", dir, e);
 				break;

org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java

@@ -203,12 +203,10 @@ class FetchProcess {
 				((BatchingProgressMonitor) monitor).setDelayStart(
 						250, TimeUnit.MILLISECONDS);
 			}
-			if (transport.isRemoveDeletedRefs())
+			if (transport.isRemoveDeletedRefs()) {
 				deleteStaleTrackingRefs(result, batch);
-			for (TrackingRefUpdate u : localUpdates) {
-				result.add(u);
-				batch.addCommand(u.asReceiveCommand());
 			}
+			addUpdateBatchCommands(result, batch);
 			for (ReceiveCommand cmd : batch.getCommands()) {
 				cmd.updateType(walk);
 				if (cmd.getType() == UPDATE_NONFASTFORWARD
@@ -221,8 +219,11 @@ class FetchProcess {
 					if (cmd.getResult() == NOT_ATTEMPTED)
 						cmd.setResult(OK);
 				}
-			} else
+			} else {
 				batch.execute(walk, monitor);
+			}
+		} catch (TransportException e) {
+			throw e;
 		} catch (IOException err) {
 			throw new TransportException(MessageFormat.format(
 					JGitText.get().failureUpdatingTrackingRef,
@@ -239,6 +240,23 @@ class FetchProcess {
 		}
 	}
 
+	private void addUpdateBatchCommands(FetchResult result,
+			BatchRefUpdate batch) throws TransportException {
+		Map<String, ObjectId> refs = new HashMap<>();
+		for (TrackingRefUpdate u : localUpdates) {
+			// Try to skip duplicates if they'd update to the same object ID
+			ObjectId existing = refs.get(u.getLocalName());
+			if (existing == null) {
+				refs.put(u.getLocalName(), u.getNewObjectId());
+				result.add(u);
+				batch.addCommand(u.asReceiveCommand());
+			} else if (!existing.equals(u.getNewObjectId())) {
+				throw new TransportException(MessageFormat
+						.format(JGitText.get().duplicateRef, u.getLocalName()));
+			}
+		}
+	}
+
 	private void fetchObjects(ProgressMonitor monitor)
 			throws TransportException {
 		try {
@@ -479,15 +497,17 @@ class FetchProcess {
 
 	private void deleteStaleTrackingRefs(FetchResult result,
 			BatchRefUpdate batch) throws IOException {
+		Set<Ref> processed = new HashSet<>();
 		for (Ref ref : localRefs().values()) {
 			if (ref.isSymbolic()) {
 				continue;
 			}
-			final String refname = ref.getName();
+			String refname = ref.getName();
 			for (RefSpec spec : toFetch) {
 				if (spec.matchDestination(refname)) {
-					final RefSpec s = spec.expandFromDestination(refname);
+					RefSpec s = spec.expandFromDestination(refname);
-					if (result.getAdvertisedRef(s.getSource()) == null) {
+					if (result.getAdvertisedRef(s.getSource()) == null
+							&& processed.add(ref)) {
 						deleteTrackingRef(result, batch, s, ref);
 					}
 				}