diff --git a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/AsIsServiceTest.java b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/AsIsServiceTest.java
index 2650db2fa..3442af94d 100644
--- a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/AsIsServiceTest.java
+++ b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/AsIsServiceTest.java
@@ -43,6 +43,8 @@
 
 package org.eclipse.jgit.http.test;
 
+import java.io.IOException;
+
 import javax.servlet.http.HttpServletRequestWrapper;
 
 import org.eclipse.jetty.server.Request;
@@ -51,6 +53,7 @@
 import org.eclipse.jgit.http.server.resolver.ServiceNotEnabledException;
 import org.eclipse.jgit.junit.LocalDiskRepositoryTestCase;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.lib.StoredConfig;
 
 public class AsIsServiceTest extends LocalDiskRepositoryTestCase {
 	private Repository db;
@@ -87,8 +90,11 @@ public void testCreate_Default() throws ServiceNotEnabledException,
 		service.access(new R("bob", "1.2.3.4"), db);
 	}
 
-	public void testCreate_Disabled() throws ServiceNotAuthorizedException {
-		db.getConfig().setBoolean("http", null, "getanyfile", false);
+	public void testCreate_Disabled() throws ServiceNotAuthorizedException,
+			IOException {
+		final StoredConfig cfg = db.getConfig();
+		cfg.setBoolean("http", null, "getanyfile", false);
+		cfg.save();
 
 		try {
 			service.access(new R(null, "1.2.3.4"), db);
diff --git a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/DefaultReceivePackFactoryTest.java b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/DefaultReceivePackFactoryTest.java
index 4d05a085c..81d5f4f51 100644
--- a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/DefaultReceivePackFactoryTest.java
+++ b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/DefaultReceivePackFactoryTest.java
@@ -43,6 +43,8 @@
 
 package org.eclipse.jgit.http.test;
 
+import java.io.IOException;
+
 import javax.servlet.http.HttpServletRequestWrapper;
 
 import org.eclipse.jetty.server.Request;
@@ -53,6 +55,7 @@
 import org.eclipse.jgit.junit.LocalDiskRepositoryTestCase;
 import org.eclipse.jgit.lib.PersonIdent;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.transport.ReceivePack;
 
 public class DefaultReceivePackFactoryTest extends LocalDiskRepositoryTestCase {
@@ -127,8 +130,11 @@ public void testCreate_AuthUser() throws ServiceNotEnabledException,
 		assertEquals(author.getWhen(), id.getWhen());
 	}
 
-	public void testCreate_Disabled() throws ServiceNotAuthorizedException {
-		db.getConfig().setBoolean("http", null, "receivepack", false);
+	public void testCreate_Disabled() throws ServiceNotAuthorizedException,
+			IOException {
+		final StoredConfig cfg = db.getConfig();
+		cfg.setBoolean("http", null, "receivepack", false);
+		cfg.save();
 
 		try {
 			factory.create(new R(null, "localhost"), db);
@@ -153,8 +159,11 @@ public void testCreate_Disabled() throws ServiceNotAuthorizedException {
 	}
 
 	public void testCreate_Enabled() throws ServiceNotEnabledException,
-			ServiceNotAuthorizedException {
-		db.getConfig().setBoolean("http", null, "receivepack", true);
+			ServiceNotAuthorizedException, IOException {
+		final StoredConfig cfg = db.getConfig();
+		cfg.setBoolean("http", null, "receivepack", true);
+		cfg.save();
+
 		ReceivePack rp;
 
 		rp = factory.create(new R(null, "1.2.3.4"), db);
diff --git a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/DefaultUploadPackFactoryTest.java b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/DefaultUploadPackFactoryTest.java
index 423361e06..24bf480dd 100644
--- a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/DefaultUploadPackFactoryTest.java
+++ b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/DefaultUploadPackFactoryTest.java
@@ -43,6 +43,8 @@
 
 package org.eclipse.jgit.http.test;
 
+import java.io.IOException;
+
 import javax.servlet.http.HttpServletRequestWrapper;
 
 import org.eclipse.jetty.server.Request;
@@ -52,6 +54,7 @@
 import org.eclipse.jgit.http.server.resolver.UploadPackFactory;
 import org.eclipse.jgit.junit.LocalDiskRepositoryTestCase;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.transport.UploadPack;
 
 public class DefaultUploadPackFactoryTest extends LocalDiskRepositoryTestCase {
@@ -104,8 +107,11 @@ public void testCreate_Default() throws ServiceNotEnabledException,
 		assertSame(db, up.getRepository());
 	}
 
-	public void testCreate_Disabled() throws ServiceNotAuthorizedException {
-		db.getConfig().setBoolean("http", null, "uploadpack", false);
+	public void testCreate_Disabled() throws ServiceNotAuthorizedException,
+			IOException {
+		final StoredConfig cfg = db.getConfig();
+		cfg.setBoolean("http", null, "uploadpack", false);
+		cfg.save();
 
 		try {
 			factory.create(new R(null, "localhost"), db);
diff --git a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/HttpClientTests.java b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/HttpClientTests.java
index c4912d405..6cf282f3b 100644
--- a/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/HttpClientTests.java
+++ b/org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/HttpClientTests.java
@@ -68,6 +68,7 @@
 import org.eclipse.jgit.lib.RefUpdate;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.revwalk.RevCommit;
+import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.storage.file.FileRepository;
 import org.eclipse.jgit.transport.FetchConnection;
 import org.eclipse.jgit.transport.Transport;
@@ -336,8 +337,9 @@ public void testListRemote_Smart_UploadPackNeedsAuth() throws Exception {
 
 	public void testListRemote_Smart_UploadPackDisabled() throws Exception {
 		FileRepository src = remoteRepository.getRepository();
-		src.getConfig().setBoolean("http", null, "uploadpack", false);
-		src.getConfig().save();
+		final FileBasedConfig cfg = src.getConfig();
+		cfg.setBoolean("http", null, "uploadpack", false);
+		cfg.save();
 
 		Repository dst = createBareRepository();
 		Transport t = Transport.open(dst, smartAuthNoneURI);
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 10396b4e7..27e0b1b54 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
@@ -47,9 +47,9 @@
 
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
-import org.eclipse.jgit.lib.Config;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.RepositoryTestCase;
+import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevTag;
 import org.eclipse.jgit.transport.RefSpec;
@@ -66,11 +66,12 @@ public void testFetch() throws JGitInternalException, IOException,
 		Git git2 = new Git(db2);
 
 		// setup the first repository to fetch from the second repository
-		final Config config = db.getConfig();
+		final StoredConfig config = db.getConfig();
 		RemoteConfig remoteConfig = new RemoteConfig(config, "test");
 		URIish uri = new URIish(db2.getDirectory().toURI().toURL());
 		remoteConfig.addURI(uri);
 		remoteConfig.update(config);
+		config.save();
 
 		// create some refs via commits and tag
 		RevCommit commit = git2.commit().setMessage("initial commit").call();
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PullCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PullCommandTest.java
index 48ede966f..5d54a1c89 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PullCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PullCommandTest.java
@@ -199,8 +199,8 @@ protected void setUp() throws Exception {
 						.getPath()));
 		config.addFetchRefSpec(new RefSpec(
 				"+refs/heads/*:refs/remotes/origin/*"));
-		targetConfig.save();
 		config.update(targetConfig);
+		targetConfig.save();
 
 		targetFile = new File(dbTarget.getWorkTree(), "SomeFile.txt");
 		writeToFile(targetFile, "Hello world");
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PushCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PushCommandTest.java
index d9a07866c..04232f6d0 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PushCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PushCommandTest.java
@@ -48,9 +48,9 @@
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.errors.MissingObjectException;
-import org.eclipse.jgit.lib.Config;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.RepositoryTestCase;
+import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevTag;
 import org.eclipse.jgit.transport.RefSpec;
@@ -66,11 +66,12 @@ public void testPush() throws JGitInternalException, IOException,
 		Repository db2 = createWorkRepository();
 
 		// setup the first repository
-		final Config config = db.getConfig();
+		final StoredConfig config = db.getConfig();
 		RemoteConfig remoteConfig = new RemoteConfig(config, "test");
 		URIish uri = new URIish(db2.getDirectory().toURI().toURL());
 		remoteConfig.addURI(uri);
 		remoteConfig.update(config);
+		config.save();
 
 		Git git1 = new Git(db);
 		// create some refs via commits and tag
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ReflogConfigTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ReflogConfigTest.java
index ded7e58fa..ea8b17df9 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ReflogConfigTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ReflogConfigTest.java
@@ -47,6 +47,8 @@
 
 import java.io.IOException;
 
+import org.eclipse.jgit.storage.file.FileBasedConfig;
+
 public class ReflogConfigTest extends RepositoryTestCase {
 	public void testlogAllRefUpdates() throws Exception {
 		long commitTime = 1154236443000L;
@@ -55,7 +57,9 @@ public void testlogAllRefUpdates() throws Exception {
 		// check that there are no entries in the reflog and turn off writing
 		// reflogs
 		assertEquals(0, db.getReflogReader(Constants.HEAD).getReverseEntries().size());
-		db.getConfig().setBoolean("core", null, "logallrefupdates", false);
+		final FileBasedConfig cfg = db.getConfig();
+		cfg.setBoolean("core", null, "logallrefupdates", false);
+		cfg.save();
 
 		// do one commit and check that reflog size is 0: no reflogs should be
 		// written
@@ -69,8 +73,9 @@ public void testlogAllRefUpdates() throws Exception {
 				db.getReflogReader(Constants.HEAD).getReverseEntries().size() == 0);
 
 		// set the logAllRefUpdates parameter to true and check it
-		db.getConfig().setBoolean("core", null, "logallrefupdates", true);
-		assertTrue(db.getConfig().get(CoreConfig.KEY).isLogAllRefUpdates());
+		cfg.setBoolean("core", null, "logallrefupdates", true);
+		cfg.save();
+		assertTrue(cfg.get(CoreConfig.KEY).isLogAllRefUpdates());
 
 		// do one commit and check that reflog size is increased to 1
 		addFileToTree(t, "i-am-another-file", "and this is other data in me\n");
@@ -82,8 +87,9 @@ public void testlogAllRefUpdates() throws Exception {
 				db.getReflogReader(Constants.HEAD).getReverseEntries().size() == 1);
 
 		// set the logAllRefUpdates parameter to false and check it
-		db.getConfig().setBoolean("core", null, "logallrefupdates", false);
-		assertFalse(db.getConfig().get(CoreConfig.KEY).isLogAllRefUpdates());
+		cfg.setBoolean("core", null, "logallrefupdates", false);
+		cfg.save();
+		assertFalse(cfg.get(CoreConfig.KEY).isLogAllRefUpdates());
 
 		// do one commit and check that reflog size is 2
 		addFileToTree(t, "i-am-anotheranother-file",