Merge branch 'stable-5.0'

* stable-5.0:
  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: I9e7fa37b100a7ea3cbe4104802d36c6f38df9e08
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

15 files changed, 331 insertions, 64 deletions

diff --git a/org.eclipse.jgit.http.apache/.settings/.api_filters b/org.eclipse.jgit.http.apache/.settings/.api_filters
deleted file mode 100644
index d1a066418c..0000000000
--- a/org.eclipse.jgit.http.apache/.settings/.api_filters
+++ /dev/null
@@ -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>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.5.target b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.5.target
index 9ae9a28491..6fad8129fa 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.5.target
+++ b/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="1534608629">
+<target name="jgit-4.5" sequenceNumber="1535206408">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.4.11.v20180605"/>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.target b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.target
index 6a6ea8d0a5..a17f16f610 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.target
+++ b/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="1534608635">
+<target name="jgit-4.6" sequenceNumber="1535206398">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.4.11.v20180605"/>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.7.target b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.7.target
index c271a1c896..c421270f75 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.7.target
+++ b/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="1534608613">
+<target name="jgit-4.7" sequenceNumber="1535206380">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.4.11.v20180605"/>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.8.target b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.8.target
index 86342dde54..2e4a812e69 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.8.target
+++ b/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="1534608610">
+<target name="jgit-4.8" sequenceNumber="1535206368">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.4.11.v20180605"/>
@@ -70,7 +70,7 @@
     </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>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.8.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.8.tpd
index 9c2d3f9270..341fbd0dc4 100644
--- a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.8.tpd
+++ b/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-9.4.11.tpd"
 include "orbit/S20180730183850-2018-09.tpd"
 
-location "http://download.eclipse.org/releases/oxygen/" {
+location "http://download.eclipse.org/releases/photon/" {
 	org.eclipse.osgi lazy
 }
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.9-staging.target b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.9-staging.target
new file mode 100644
index 0000000000..9064c1b32c
--- /dev/null
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.9-staging.target
@@ -0,0 +1,76 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<?pde?>
+<!-- generated with https://github.com/mbarbero/fr.obeo.releng.targetplatform -->
+<target name="jgit-4.9-staging" sequenceNumber="1535206361">
+  <locations>
+    <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
+      <unit id="org.eclipse.jetty.client" version="9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.client.source" version="9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.continuation" version="9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.continuation.source" version="9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.http" version="9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.http.source" version="9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.io" version="9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.io.source" version="9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.security" version="9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.security.source" version="9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.server" version="9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.server.source" version="9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.servlet" version="9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.servlet.source" version="9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.util" version="9.4.11.v20180605"/>
+      <unit id="org.eclipse.jetty.util.source" version="9.4.11.v20180605"/>
+      <repository id="jetty-9.4.11" location="http://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.11.v20180605"/>
+    </location>
+    <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
+      <unit id="org.apache.ant" version="1.9.6.v201510161327"/>
+      <unit id="org.apache.ant.source" version="1.9.6.v201510161327"/>
+      <unit id="org.apache.commons.codec" version="1.10.0.v20180409-1845"/>
+      <unit id="org.apache.commons.codec.source" version="1.10.0.v20180409-1845"/>
+      <unit id="org.apache.commons.compress" version="1.15.0.v20180119-1613"/>
+      <unit id="org.apache.commons.compress.source" version="1.15.0.v20180119-1613"/>
+      <unit id="org.apache.commons.logging" version="1.2.0.v20180409-1502"/>
+      <unit id="org.apache.commons.logging.source" version="1.2.0.v20180409-1502"/>
+      <unit id="org.apache.httpcomponents.httpclient" version="4.5.5.v20180409-1525"/>
+      <unit id="org.apache.httpcomponents.httpclient.source" version="4.5.5.v20180409-1525"/>
+      <unit id="org.apache.httpcomponents.httpcore" version="4.4.9.v20180409-1525"/>
+      <unit id="org.apache.httpcomponents.httpcore.source" version="4.4.9.v20180409-1525"/>
+      <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"/>
+      <unit id="org.kohsuke.args4j.source" version="2.33.0.v20160323-2218"/>
+      <unit id="org.hamcrest" version="1.1.0.v20090501071000"/>
+      <unit id="org.hamcrest.core" version="1.3.0.v20180420-1519"/>
+      <unit id="org.hamcrest.core.source" version="1.3.0.v20180420-1519"/>
+      <unit id="org.hamcrest.library" version="1.3.0.v20180524-2246"/>
+      <unit id="org.hamcrest.library.source" version="1.3.0.v20180524-2246"/>
+      <unit id="javaewah" version="1.1.6.v20160919-1400"/>
+      <unit id="javaewah.source" version="1.1.6.v20160919-1400"/>
+      <unit id="org.objenesis" version="1.0.0.v201505121915"/>
+      <unit id="org.objenesis.source" version="1.0.0.v201505121915"/>
+      <unit id="org.mockito" version="1.8.4.v201303031500"/>
+      <unit id="org.mockito.source" version="1.8.4.v201303031500"/>
+      <unit id="com.google.gson" version="2.8.2.v20180104-1110"/>
+      <unit id="com.google.gson.source" version="2.8.2.v20180104-1110"/>
+      <unit id="com.jcraft.jsch" version="0.1.54.v20170116-1932"/>
+      <unit id="com.jcraft.jsch.source" version="0.1.54.v20170116-1932"/>
+      <unit id="org.junit" version="4.12.0.v201504281640"/>
+      <unit id="org.junit.source" version="4.12.0.v201504281640"/>
+      <unit id="javax.servlet" version="3.1.0.v201410161800"/>
+      <unit id="javax.servlet.source" version="3.1.0.v201410161800"/>
+      <unit id="org.tukaani.xz" version="1.6.0.v20170629-1752"/>
+      <unit id="org.tukaani.xz.source" version="1.6.0.v20170629-1752"/>
+      <unit id="org.slf4j.api" version="1.7.2.v20121108-1250"/>
+      <unit id="org.slf4j.api.source" version="1.7.2.v20121108-1250"/>
+      <unit id="org.slf4j.impl.log4j12" version="1.7.2.v20131105-2200"/>
+      <unit id="org.slf4j.impl.log4j12.source" version="1.7.2.v20131105-2200"/>
+      <unit id="com.jcraft.jzlib" version="1.1.1.v201205102305"/>
+      <unit id="com.jcraft.jzlib.source" version="1.1.1.v201205102305"/>
+      <repository location="http://download.eclipse.org/tools/orbit/downloads/drops/S20180730183850/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/staging/2018-09/"/>
+    </location>
+  </locations>
+</target>
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.9-staging.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.9-staging.tpd
new file mode 100644
index 0000000000..2319e92740
--- /dev/null
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.9-staging.tpd
@@ -0,0 +1,8 @@
+target "jgit-4.9-staging" with source configurePhase
+
+include "projects/jetty-9.4.11.tpd"
+include "orbit/S20180730183850-2018-09.tpd"
+
+location "http://download.eclipse.org/staging/2018-09/" {
+	org.eclipse.osgi lazy
+}
\ No newline at end of file
diff --git a/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20180606145124-Photon.tpd b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20180606145124-Photon.tpd
new file mode 100644
index 0000000000..ecec41d8c6
--- /dev/null
+++ b/org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20180606145124-Photon.tpd
@@ -0,0 +1,48 @@
+target "R20180606145124-Photon" with source configurePhase
+// see http://download.eclipse.org/tools/orbit/downloads/
+
+location "http://download.eclipse.org/tools/orbit/downloads/drops/R20180606145124/repository" {
+	org.apache.ant [1.9.6.v201510161327,1.9.6.v201510161327]
+	org.apache.ant.source [1.9.6.v201510161327,1.9.6.v201510161327]
+	org.apache.commons.codec [1.9.0.v20170208-1614,1.9.0.v20170208-1614]
+	org.apache.commons.codec.source [1.9.0.v20170208-1614,1.9.0.v20170208-1614]
+	org.apache.commons.compress [1.15.0.v20180119-1613,1.15.0.v20180119-1613]
+	org.apache.commons.compress.source [1.15.0.v20180119-1613,1.15.0.v20180119-1613s]
+	org.apache.commons.logging [1.1.1.v201101211721,1.1.1.v201101211721]
+	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]
+	org.kohsuke.args4j.source [2.33.0.v20160323-2218,2.33.0.v20160323-2218]
+	org.hamcrest [1.1.0.v20090501071000,1.1.0.v20090501071000]
+	org.hamcrest.core [1.3.0.v20180420-1519,1.3.0.v20180420-1519]
+	org.hamcrest.core.source [1.3.0.v20180420-1519,1.3.0.v20180420-1519]
+	org.hamcrest.library [1.3.0.v20180524-2246,1.3.0.v20180524-2246]
+	org.hamcrest.library.source [1.3.0.v20180524-2246,1.3.0.v20180524-2246]
+	javaewah [1.1.6.v20160919-1400,1.1.6.v20160919-1400]
+	javaewah.source [1.1.6.v20160919-1400,1.1.6.v20160919-1400]
+	org.objenesis [1.0.0.v201505121915,1.0.0.v201505121915]
+	org.objenesis.source [1.0.0.v201505121915,1.0.0.v201505121915]
+	org.mockito [1.8.4.v201303031500,1.8.4.v201303031500]
+	org.mockito.source [1.8.4.v201303031500,1.8.4.v201303031500]
+	com.google.gson [2.8.2.v20180104-1110,2.8.2.v20180104-1110]
+	com.google.gson.source [2.8.2.v20180104-1110,2.8.2.v20180104-1110]
+	com.jcraft.jsch [0.1.54.v20170116-1932,0.1.54.v20170116-1932]
+	com.jcraft.jsch.source [0.1.54.v20170116-1932,0.1.54.v20170116-1932]
+	org.junit [4.12.0.v201504281640,4.12.0.v201504281640]
+	org.junit.source [4.12.0.v201504281640,4.12.0.v201504281640]
+	javax.servlet [3.1.0.v201410161800,3.1.0.v201410161800]
+	javax.servlet.source [3.1.0.v201410161800,3.1.0.v201410161800]
+	org.tukaani.xz [1.6.0.v20170629-1752,1.6.0.v20170629-1752]
+	org.tukaani.xz.source [1.6.0.v20170629-1752,1.6.0.v20170629-1752]
+	org.slf4j.api [1.7.2.v20121108-1250,1.7.2.v20121108-1250]
+	org.slf4j.api.source [1.7.2.v20121108-1250,1.7.2.v20121108-1250]
+	org.slf4j.impl.log4j12 [1.7.2.v20131105-2200,1.7.2.v20131105-2200]
+	org.slf4j.impl.log4j12.source [1.7.2.v20131105-2200,1.7.2.v20131105-2200]
+	com.jcraft.jzlib [1.1.1.v201205102305,1.1.1.v201205102305]
+	com.jcraft.jzlib.source [1.1.1.v201205102305,1.1.1.v201205102305]
+}
diff --git a/org.eclipse.jgit.pgm/.settings/.api_filters b/org.eclipse.jgit.pgm/.settings/.api_filters
deleted file mode 100644
index facef2df6b..0000000000
--- a/org.eclipse.jgit.pgm/.settings/.api_filters
+++ /dev/null
@@ -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>
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 4c2c0e8d1f..adc4d98488 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
@@ -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;
@@ -126,6 +129,91 @@ public class FetchCommandTest extends RepositoryTestCase {
 	}
 
 	@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();
 		Ref tagRef = remoteGit.tag().setName("foo").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));
+	}
 }
diff --git a/org.eclipse.jgit.ui/.settings/.api_filters b/org.eclipse.jgit.ui/.settings/.api_filters
deleted file mode 100644
index aed9c7a352..0000000000
--- a/org.eclipse.jgit.ui/.settings/.api_filters
+++ /dev/null
@@ -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>
diff --git a/org.eclipse.jgit/.settings/.api_filters b/org.eclipse.jgit/.settings/.api_filters
index b7b49bc658..9f4b761495 100644
--- a/org.eclipse.jgit/.settings/.api_filters
+++ b/org.eclipse.jgit/.settings/.api_filters
@@ -7,22 +7,6 @@
             </message_arguments>
         </filter>
     </resource>
-    <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>
     <resource path="src/org/eclipse/jgit/transport/GitProtocolConstants.java" type="org.eclipse.jgit.transport.GitProtocolConstants">
         <filter id="337768515">
             <message_arguments>
@@ -30,4 +14,4 @@
             </message_arguments>
         </filter>
     </resource>
-</component>
+</component>
\ No newline at end of file
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
index 7d2bd4897a..40c6de33fa 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
+++ b/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); //$NON-NLS-1$
 				break;
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 ff183c8974..c43ab18c35 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
+++ b/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);
-					if (result.getAdvertisedRef(s.getSource()) == null) {
+					RefSpec s = spec.expandFromDestination(refname);
+					if (result.getAdvertisedRef(s.getSource()) == null
+							&& processed.add(ref)) {
 						deleteTrackingRef(result, batch, s, ref);
 					}
 				}