Merge branch 'stable-3.2'

* stable-3.2:
  Canonicalize worktree path in BaseRepositoryBuilder if set via config
  Add missing @since tags for new public methods in Config
  Don't use API exception in RebaseTodoLine
  Fix aborting rebase with detached head
  Add recursive variant of Config.getNames() methods
  Prepare post 3.2.0-m3 builds
  JGit v3.2.0.201311130903-m3

Change-Id: Iad6e284e0fe2c7950f156372b334e47ebd82f3f7
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

8 files changed, 361 insertions, 59 deletions

diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RebaseCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RebaseCommandTest.java
index a61b44eda8..a728cd2461 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RebaseCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/RebaseCommandTest.java
@@ -64,13 +64,13 @@ import org.eclipse.jgit.api.RebaseCommand.InteractiveHandler;
 import org.eclipse.jgit.api.RebaseCommand.Operation;
 import org.eclipse.jgit.api.RebaseResult.Status;
 import org.eclipse.jgit.api.errors.InvalidRebaseStepException;
-import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.api.errors.RefNotFoundException;
 import org.eclipse.jgit.api.errors.UnmergedPathsException;
 import org.eclipse.jgit.api.errors.WrongRepositoryStateException;
 import org.eclipse.jgit.diff.DiffEntry;
 import org.eclipse.jgit.dircache.DirCacheCheckout;
 import org.eclipse.jgit.errors.AmbiguousObjectException;
+import org.eclipse.jgit.errors.IllegalTodoFileModification;
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
 import org.eclipse.jgit.errors.MissingObjectException;
 import org.eclipse.jgit.junit.RepositoryTestCase;
@@ -576,6 +576,69 @@ public class RebaseCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
+	public void testStopOnConflictAndAbortWithDetachedHEAD() throws Exception {
+		// create file1 on master
+		RevCommit firstInMaster = writeFileAndCommit(FILE1, "Add file1", "1",
+				"2", "3");
+		// change first line in master
+		writeFileAndCommit(FILE1, "change file1 in master", "1master", "2", "3");
+		checkFile(FILE1, "1master", "2", "3");
+		// create a topic branch based on second commit
+		createBranch(firstInMaster, "refs/heads/topic");
+		checkoutBranch("refs/heads/topic");
+		// we have the old content again
+		checkFile(FILE1, "1", "2", "3");
+
+		// add a line (non-conflicting)
+		writeFileAndCommit(FILE1, "add a line to file1 in topic", "1", "2",
+				"3", "topic4");
+
+		// change first line (conflicting)
+		RevCommit conflicting = writeFileAndCommit(FILE1,
+				"change file1 in topic", "1topic", "2", "3", "topic4");
+
+		RevCommit lastTopicCommit = writeFileAndCommit(FILE1,
+				"change file1 in topic again", "1topic", "2", "3", "topic4");
+
+		git.checkout().setName(lastTopicCommit.getName()).call();
+
+		RebaseResult res = git.rebase().setUpstream("refs/heads/master").call();
+		assertEquals(Status.STOPPED, res.getStatus());
+		assertEquals(conflicting, res.getCurrentCommit());
+		checkFile(FILE1,
+				"<<<<<<< Upstream, based on master\n1master\n=======\n1topic",
+				">>>>>>> e0d1dea change file1 in topic\n2\n3\ntopic4");
+
+		assertEquals(RepositoryState.REBASING_INTERACTIVE,
+				db.getRepositoryState());
+		assertTrue(new File(db.getDirectory(), "rebase-merge").exists());
+		// the first one should be included, so we should have left two picks in
+		// the file
+		assertEquals(1, countPicks());
+
+		// rebase should not succeed in this state
+		try {
+			git.rebase().setUpstream("refs/heads/master").call();
+			fail("Expected exception was not thrown");
+		} catch (WrongRepositoryStateException e) {
+			// expected
+		}
+
+		// abort should reset to topic branch
+		res = git.rebase().setOperation(Operation.ABORT).call();
+		assertEquals(res.getStatus(), Status.ABORTED);
+		assertEquals(lastTopicCommit.getName(), db.getFullBranch());
+		checkFile(FILE1, "1topic", "2", "3", "topic4");
+		RevWalk rw = new RevWalk(db);
+		assertEquals(lastTopicCommit,
+				rw.parseCommit(db.resolve(Constants.HEAD)));
+		assertEquals(RepositoryState.SAFE, db.getRepositoryState());
+
+		// rebase- dir in .git must be deleted
+		assertFalse(new File(db.getDirectory(), "rebase-merge").exists());
+	}
+
+	@Test
 	public void testStopOnConflictAndContinue() throws Exception {
 		// create file1 on master
 		RevCommit firstInMaster = writeFileAndCommit(FILE1, "Add file1", "1",
@@ -1890,8 +1953,12 @@ public class RebaseCommandTest extends RepositoryTestCase {
 		RebaseResult res2 = git.rebase().setUpstream("HEAD~2")
 				.runInteractively(new InteractiveHandler() {
 					public void prepareSteps(List<RebaseTodoLine> steps) {
-						steps.get(0).setAction(Action.COMMENT); // delete
-																// RevCommit c4
+						try {
+							// delete RevCommit c4
+							steps.get(0).setAction(Action.COMMENT);
+						} catch (IllegalTodoFileModification e) {
+							fail("unexpected exception: " + e);
+						}
 					}
 
 					public String modifyCommitMessage(String commit) {
@@ -2020,7 +2087,7 @@ public class RebaseCommandTest extends RepositoryTestCase {
 		try {
 			new RebaseTodoLine("This is a invalid comment");
 			fail("Constructing a comment line with invalid comment string should fail, but doesn't");
-		} catch (JGitInternalException e) {
+		} catch (IllegalArgumentException e) {
 			// expected
 		}
 		RebaseTodoLine validCommentLine = new RebaseTodoLine(
@@ -2035,7 +2102,7 @@ public class RebaseCommandTest extends RepositoryTestCase {
 		try {
 			actionLineToBeChanged.setComment("invalid comment");
 			fail("Setting a invalid comment string should fail but doesn't");
-		} catch (JGitInternalException e) {
+		} catch (IllegalArgumentException e) {
 			assertEquals(null, actionLineToBeChanged.getComment());
 		}
 
@@ -2044,7 +2111,7 @@ public class RebaseCommandTest extends RepositoryTestCase {
 		try {
 			actionLineToBeChanged.setComment("invalid comment");
 			fail("Setting a invalid comment string should fail but doesn't");
-		} catch (JGitInternalException e) {
+		} catch (IllegalArgumentException e) {
 			// expected
 			// setting comment failed, but was successfully set before,
 			// therefore it may not be altered since then
@@ -2061,7 +2128,7 @@ public class RebaseCommandTest extends RepositoryTestCase {
 			actionLineToBeChanged.setComment("line1 \n\r line2");
 			actionLineToBeChanged.setComment("\n\r");
 			fail("Setting a multiline comment string should fail but doesn't");
-		} catch (JGitInternalException e) {
+		} catch (IllegalArgumentException e) {
 			// expected
 		}
 		// Try setting valid comments
@@ -2113,9 +2180,15 @@ public class RebaseCommandTest extends RepositoryTestCase {
 
 		RebaseResult res = git.rebase().setUpstream("HEAD~2")
 				.runInteractively(new InteractiveHandler() {
+
 					public void prepareSteps(List<RebaseTodoLine> steps) {
-						steps.get(0).setAction(Action.REWORD);
+						try {
+							steps.get(0).setAction(Action.REWORD);
+						} catch (IllegalTodoFileModification e) {
+							fail("unexpected exception: " + e);
+						}
 					}
+
 					public String modifyCommitMessage(String commit) {
 						return "rewritten commit message";
 					}
@@ -2155,7 +2228,11 @@ public class RebaseCommandTest extends RepositoryTestCase {
 		RebaseResult res = git.rebase().setUpstream("HEAD~2")
 				.runInteractively(new InteractiveHandler() {
 					public void prepareSteps(List<RebaseTodoLine> steps) {
-						steps.get(0).setAction(Action.EDIT);
+						try {
+							steps.get(0).setAction(Action.EDIT);
+						} catch (IllegalTodoFileModification e) {
+							fail("unexpected exception: " + e);
+						}
 					}
 
 					public String modifyCommitMessage(String commit) {
@@ -2215,7 +2292,11 @@ public class RebaseCommandTest extends RepositoryTestCase {
 				.runInteractively(new InteractiveHandler() {
 
 					public void prepareSteps(List<RebaseTodoLine> steps) {
-						steps.get(1).setAction(Action.SQUASH);
+						try {
+							steps.get(1).setAction(Action.SQUASH);
+						} catch (IllegalTodoFileModification e) {
+							fail("unexpected exception: " + e);
+						}
 					}
 
 					public String modifyCommitMessage(String commit) {
@@ -2290,8 +2371,12 @@ public class RebaseCommandTest extends RepositoryTestCase {
 				.runInteractively(new InteractiveHandler() {
 
 					public void prepareSteps(List<RebaseTodoLine> steps) {
-						steps.get(1).setAction(Action.SQUASH);
-						steps.get(2).setAction(Action.SQUASH);
+						try {
+							steps.get(1).setAction(Action.SQUASH);
+							steps.get(2).setAction(Action.SQUASH);
+						} catch (IllegalTodoFileModification e) {
+							fail("unexpected exception: " + e);
+						}
 					}
 
 					public String modifyCommitMessage(String commit) {
@@ -2367,8 +2452,12 @@ public class RebaseCommandTest extends RepositoryTestCase {
 				.runInteractively(new InteractiveHandler() {
 
 					public void prepareSteps(List<RebaseTodoLine> steps) {
-						steps.get(1).setAction(Action.FIXUP);
-						steps.get(2).setAction(Action.SQUASH);
+						try {
+							steps.get(1).setAction(Action.FIXUP);
+							steps.get(2).setAction(Action.SQUASH);
+						} catch (IllegalTodoFileModification e) {
+							fail("unexpected exception: " + e);
+						}
 					}
 
 					public String modifyCommitMessage(String commit) {
@@ -2437,7 +2526,11 @@ public class RebaseCommandTest extends RepositoryTestCase {
 				.runInteractively(new InteractiveHandler() {
 
 					public void prepareSteps(List<RebaseTodoLine> steps) {
-						steps.get(1).setAction(Action.FIXUP);
+						try {
+							steps.get(1).setAction(Action.FIXUP);
+						} catch (IllegalTodoFileModification e) {
+							fail("unexpected exception: " + e);
+						}
 					}
 
 					public String modifyCommitMessage(String commit) {
@@ -2481,7 +2574,11 @@ public class RebaseCommandTest extends RepositoryTestCase {
 				.runInteractively(new InteractiveHandler() {
 
 					public void prepareSteps(List<RebaseTodoLine> steps) {
-						steps.get(1).setAction(Action.FIXUP);
+						try {
+							steps.get(1).setAction(Action.FIXUP);
+						} catch (IllegalTodoFileModification e) {
+							fail("unexpected exception: " + e);
+						}
 					}
 
 					public String modifyCommitMessage(String commit) {
@@ -2516,7 +2613,11 @@ public class RebaseCommandTest extends RepositoryTestCase {
 				.runInteractively(new InteractiveHandler() {
 
 					public void prepareSteps(List<RebaseTodoLine> steps) {
-						steps.get(0).setAction(Action.FIXUP);
+						try {
+							steps.get(0).setAction(Action.FIXUP);
+						} catch (IllegalTodoFileModification e) {
+							fail("unexpected exception: " + e);
+						}
 					}
 
 					public String modifyCommitMessage(String commit) {
@@ -2544,7 +2645,11 @@ public class RebaseCommandTest extends RepositoryTestCase {
 				.runInteractively(new InteractiveHandler() {
 
 					public void prepareSteps(List<RebaseTodoLine> steps) {
-						steps.get(0).setAction(Action.SQUASH);
+						try {
+							steps.get(0).setAction(Action.SQUASH);
+						} catch (IllegalTodoFileModification e) {
+							fail("unexpected exception: " + e);
+						}
 					}
 
 					public String modifyCommitMessage(String commit) {
@@ -2571,7 +2676,11 @@ public class RebaseCommandTest extends RepositoryTestCase {
 				.runInteractively(new InteractiveHandler() {
 
 					public void prepareSteps(List<RebaseTodoLine> steps) {
-						steps.get(0).setAction(Action.EDIT);
+						try {
+							steps.get(0).setAction(Action.EDIT);
+						} catch (IllegalTodoFileModification e) {
+							fail("unexpected exception: " + e);
+						}
 					}
 
 					public String modifyCommitMessage(String commit) {
@@ -2610,7 +2719,11 @@ public class RebaseCommandTest extends RepositoryTestCase {
 
 					public void prepareSteps(List<RebaseTodoLine> steps) {
 						steps.remove(0);
-						steps.get(0).setAction(Action.EDIT);
+						try {
+							steps.get(0).setAction(Action.EDIT);
+						} catch (IllegalTodoFileModification e) {
+							fail("unexpected exception: " + e);
+						}
 					}
 
 					public String modifyCommitMessage(String commit) {
@@ -2648,7 +2761,11 @@ public class RebaseCommandTest extends RepositoryTestCase {
 
 					public void prepareSteps(List<RebaseTodoLine> steps) {
 						steps.remove(0);
-						steps.get(0).setAction(Action.REWORD);
+						try {
+							steps.get(0).setAction(Action.REWORD);
+						} catch (IllegalTodoFileModification e) {
+							fail("unexpected exception: " + e);
+						}
 					}
 
 					public String modifyCommitMessage(String commit) {
@@ -2661,7 +2778,11 @@ public class RebaseCommandTest extends RepositoryTestCase {
 
 			public void prepareSteps(List<RebaseTodoLine> steps) {
 				steps.remove(0);
-				steps.get(0).setAction(Action.REWORD);
+				try {
+					steps.get(0).setAction(Action.REWORD);
+				} catch (IllegalTodoFileModification e) {
+					fail("unexpected exception: " + e);
+				}
 			}
 
 			public String modifyCommitMessage(String commit) {
@@ -2702,9 +2823,13 @@ public class RebaseCommandTest extends RepositoryTestCase {
 				.runInteractively(new InteractiveHandler() {
 
 					public void prepareSteps(List<RebaseTodoLine> steps) {
-						steps.get(0).setAction(Action.PICK);
-						steps.remove(1);
-						steps.get(1).setAction(Action.SQUASH);
+						try {
+							steps.get(0).setAction(Action.PICK);
+							steps.remove(1);
+							steps.get(1).setAction(Action.SQUASH);
+						} catch (IllegalTodoFileModification e) {
+							fail("unexpected exception: " + e);
+						}
 					}
 
 					public String modifyCommitMessage(String commit) {
@@ -2716,9 +2841,13 @@ public class RebaseCommandTest extends RepositoryTestCase {
 		result = git.rebase().runInteractively(new InteractiveHandler() {
 
 			public void prepareSteps(List<RebaseTodoLine> steps) {
-				steps.get(0).setAction(Action.PICK);
-				steps.remove(1);
-				steps.get(1).setAction(Action.SQUASH);
+				try {
+					steps.get(0).setAction(Action.PICK);
+					steps.remove(1);
+					steps.get(1).setAction(Action.SQUASH);
+				} catch (IllegalTodoFileModification e) {
+					fail("unexpected exception: " + e);
+				}
 			}
 
 			public String modifyCommitMessage(String commit) {
@@ -2760,9 +2889,13 @@ public class RebaseCommandTest extends RepositoryTestCase {
 				.runInteractively(new InteractiveHandler() {
 
 					public void prepareSteps(List<RebaseTodoLine> steps) {
-						steps.get(0).setAction(Action.PICK);
-						steps.remove(1);
-						steps.get(1).setAction(Action.FIXUP);
+						try {
+							steps.get(0).setAction(Action.PICK);
+							steps.remove(1);
+							steps.get(1).setAction(Action.FIXUP);
+						} catch (IllegalTodoFileModification e) {
+							fail("unexpected exception: " + e);
+						}
 					}
 
 					public String modifyCommitMessage(String commit) {
@@ -2774,9 +2907,13 @@ public class RebaseCommandTest extends RepositoryTestCase {
 		result = git.rebase().runInteractively(new InteractiveHandler() {
 
 			public void prepareSteps(List<RebaseTodoLine> steps) {
-				steps.get(0).setAction(Action.PICK);
-				steps.remove(1);
-				steps.get(1).setAction(Action.FIXUP);
+				try {
+					steps.get(0).setAction(Action.PICK);
+					steps.remove(1);
+					steps.get(1).setAction(Action.FIXUP);
+				} catch (IllegalTodoFileModification e) {
+					fail("unexpected exception: " + e);
+				}
 			}
 
 			public String modifyCommitMessage(String commit) {
@@ -2823,8 +2960,12 @@ public class RebaseCommandTest extends RepositoryTestCase {
 				.runInteractively(new InteractiveHandler() {
 
 					public void prepareSteps(List<RebaseTodoLine> steps) {
-						steps.get(0).setAction(Action.EDIT);
-						steps.get(1).setAction(Action.PICK);
+						try {
+							steps.get(0).setAction(Action.EDIT);
+							steps.get(1).setAction(Action.PICK);
+						} catch (IllegalTodoFileModification e) {
+							fail("unexpected exception: " + e);
+						}
 					}
 
 					public String modifyCommitMessage(String commit) {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ConfigTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ConfigTest.java
index 6ebef6cbf9..630bd7dc0d 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ConfigTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ConfigTest.java
@@ -520,6 +520,31 @@ public class ConfigTest {
 	}
 
 	@Test
+	public void test_ReadNamesInSectionRecursive()
+			throws ConfigInvalidException {
+		String baseConfigString = "[core]\n" + "logAllRefUpdates = true\n";
+		String configString = "[core]\n" + "repositoryFormatVersion = 0\n"
+				+ "filemode = false\n";
+		final Config c = parse(configString, parse(baseConfigString));
+		Set<String> names = c.getNames("core", true);
+		assertEquals("Core section size", 3, names.size());
+		assertTrue("Core section should contain \"filemode\"",
+				names.contains("filemode"));
+		assertTrue("Core section should contain \"repositoryFormatVersion\"",
+				names.contains("repositoryFormatVersion"));
+		assertTrue("Core section should contain \"logAllRefUpdates\"",
+				names.contains("logAllRefUpdates"));
+		assertTrue("Core section should contain \"logallrefupdates\"",
+				names.contains("logallrefupdates"));
+
+		Iterator<String> itr = names.iterator();
+		assertEquals("filemode", itr.next());
+		assertEquals("repositoryFormatVersion", itr.next());
+		assertEquals("logAllRefUpdates", itr.next());
+		assertFalse(itr.hasNext());
+	}
+
+	@Test
 	public void test010_readNamesInSubSection() throws ConfigInvalidException {
 		String configString = "[a \"sub1\"]\n"//
 				+ "x = 0\n" //
@@ -541,6 +566,30 @@ public class ConfigTest {
 	}
 
 	@Test
+	public void readNamesInSubSectionRecursive() throws ConfigInvalidException {
+		String baseConfigString = "[a \"sub1\"]\n"//
+				+ "x = 0\n" //
+				+ "y = false\n"//
+				+ "[a \"sub2\"]\n"//
+				+ "A=0\n";//
+		String configString = "[a \"sub1\"]\n"//
+				+ "z = true\n"//
+				+ "[a \"sub2\"]\n"//
+				+ "B=1\n";
+		final Config c = parse(configString, parse(baseConfigString));
+		Set<String> names = c.getNames("a", "sub1", true);
+		assertEquals("Subsection size", 3, names.size());
+		assertTrue("Subsection should contain \"x\"", names.contains("x"));
+		assertTrue("Subsection should contain \"y\"", names.contains("y"));
+		assertTrue("Subsection should contain \"z\"", names.contains("z"));
+		names = c.getNames("a", "sub2", true);
+		assertEquals("Subsection size", 2, names.size());
+		assertTrue("Subsection should contain \"A\"", names.contains("A"));
+		assertTrue("Subsection should contain \"a\"", names.contains("a"));
+		assertTrue("Subsection should contain \"B\"", names.contains("B"));
+	}
+
+	@Test
 	public void testQuotingForSubSectionNames() {
 		String resultPattern = "[testsection \"{0}\"]\n\ttestname = testvalue\n";
 		String result;
@@ -584,7 +633,12 @@ public class ConfigTest {
 
 	private static Config parse(final String content)
 			throws ConfigInvalidException {
-		final Config c = new Config(null);
+		return parse(content, null);
+	}
+
+	private static Config parse(final String content, Config baseConfig)
+			throws ConfigInvalidException {
+		final Config c = new Config(baseConfig);
 		c.fromText(content);
 		return c;
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
index 10b273a744..ac6f5487a1 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
@@ -1101,24 +1101,29 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 		}
 		try {
 			String headName = rebaseState.readFile(HEAD_NAME);
-			if (headName.startsWith(Constants.R_REFS)) {
 				monitor.beginTask(MessageFormat.format(
 						JGitText.get().resettingHead, headName),
 						ProgressMonitor.UNKNOWN);
 
+			Result res = null;
+			RefUpdate refUpdate = repo.updateRef(Constants.HEAD, false);
+			refUpdate.setRefLogMessage("rebase: aborting", false); //$NON-NLS-1$
+			if (headName.startsWith(Constants.R_REFS)) {
 				// update the HEAD
-				RefUpdate refUpdate = repo.updateRef(Constants.HEAD, false);
-				refUpdate.setRefLogMessage("rebase: aborting", false); //$NON-NLS-1$
-				Result res = refUpdate.link(headName);
-				switch (res) {
-				case FAST_FORWARD:
-				case FORCED:
-				case NO_CHANGE:
-					break;
-				default:
-					throw new JGitInternalException(
-							JGitText.get().abortingRebaseFailed);
-				}
+				res = refUpdate.link(headName);
+			} else {
+				refUpdate.setNewObjectId(repo.readOrigHead());
+				res = refUpdate.forceUpdate();
+
+			}
+			switch (res) {
+			case FAST_FORWARD:
+			case FORCED:
+			case NO_CHANGE:
+				break;
+			default:
+				throw new JGitInternalException(
+						JGitText.get().abortingRebaseFailed);
 			}
 			boolean stashConflicts = autoStashApply();
 			// cleanup the files
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/errors/IllegalTodoFileModification.java b/org.eclipse.jgit/src/org/eclipse/jgit/errors/IllegalTodoFileModification.java
new file mode 100644
index 0000000000..dae150ce0a
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/errors/IllegalTodoFileModification.java
@@ -0,0 +1,59 @@
+/*
+ * Copyright (C) 2013, Christian Halstrick <christian.halstrick@sap.com>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.errors;
+
+/**
+ * Attempt to modify a rebase-todo file in an unsupported way
+ *
+ * @since 3.2
+ */
+public class IllegalTodoFileModification extends Exception {
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * @param msg
+	 */
+	public IllegalTodoFileModification(final String msg) {
+		super(msg);
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/BaseRepositoryBuilder.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/BaseRepositoryBuilder.java
index db622f319d..7a6ddb39a1 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/BaseRepositoryBuilder.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/BaseRepositoryBuilder.java
@@ -695,7 +695,7 @@ public class BaseRepositoryBuilder<B extends BaseRepositoryBuilder, R extends Re
 		String path = cfg.getString(CONFIG_CORE_SECTION, null,
 				CONFIG_KEY_WORKTREE);
 		if (path != null)
-			return safeFS().resolve(getGitDir(), path);
+			return safeFS().resolve(getGitDir(), path).getCanonicalFile();
 
 		// If core.bare is set, honor its value. Assume workTree is
 		// the parent directory of the repository.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java
index 81977d74ac..22337e8131 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java
@@ -528,6 +528,35 @@ public class Config {
 	}
 
 	/**
+	 * @param section
+	 *            the section
+	 * @param recursive
+	 *            if {@code true} recursively adds the names defined in all base
+	 *            configurations
+	 * @return the list of names defined for this section
+	 * @since 3.2
+	 */
+	public Set<String> getNames(String section, boolean recursive) {
+		return getState().getNames(section, null, recursive);
+	}
+
+	/**
+	 * @param section
+	 *            the section
+	 * @param subsection
+	 *            the subsection
+	 * @param recursive
+	 *            if {@code true} recursively adds the names defined in all base
+	 *            configurations
+	 * @return the list of names defined for this subsection
+	 * @since 3.2
+	 */
+	public Set<String> getNames(String section, String subsection,
+			boolean recursive) {
+		return getState().getNames(section, subsection, recursive);
+	}
+
+	/**
 	 * Obtain a handle to a parsed set of configuration values.
 	 *
 	 * @param <T>
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigSnapshot.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigSnapshot.java
index b7c4c64321..5ed129ed02 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigSnapshot.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigSnapshot.java
@@ -97,6 +97,16 @@ class ConfigSnapshot {
 	}
 
 	Set<String> getNames(String section, String subsection) {
+		return getNames(section, subsection, false);
+	}
+
+	Set<String> getNames(String section, String subsection, boolean recursive) {
+		Map<String, String> m = getNamesInternal(section, subsection, recursive);
+		return new CaseFoldingSet(m);
+	}
+
+	private Map<String, String> getNamesInternal(String section,
+			String subsection, boolean recursive) {
 		List<ConfigLine> s = sorted();
 		int idx = find(s, section, subsection, ""); //$NON-NLS-1$
 		if (idx < 0)
@@ -113,7 +123,9 @@ class ConfigSnapshot {
 			if (!m.containsKey(l))
 				m.put(l, e.name);
 		}
-		return new CaseFoldingSet(m);
+		if (recursive && baseState != null)
+			m.putAll(baseState.getNamesInternal(section, subsection, recursive));
+		return m;
 	}
 
 	String[] get(String section, String subsection, String name) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RebaseTodoLine.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RebaseTodoLine.java
index 3aa331c72c..9af8d76910 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RebaseTodoLine.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RebaseTodoLine.java
@@ -45,7 +45,7 @@ package org.eclipse.jgit.lib;
 
 import java.text.MessageFormat;
 
-import org.eclipse.jgit.api.errors.JGitInternalException;
+import org.eclipse.jgit.errors.IllegalTodoFileModification;
 import org.eclipse.jgit.internal.JGitText;
 
 /**
@@ -111,7 +111,7 @@ public class RebaseTodoLine {
 						|| action.shortToken.equals(token))
 					return action;
 			}
-			throw new JGitInternalException(MessageFormat.format(
+			throw new IllegalArgumentException(MessageFormat.format(
 					JGitText.get().unknownOrUnsupportedCommand, token,
 					Action.values()));
 		}
@@ -167,8 +167,11 @@ public class RebaseTodoLine {
 	 * non-comment.
 	 *
 	 * @param newAction
+	 * @throws IllegalTodoFileModification
+	 *             on attempt to set a non-comment action on a line which was a
+	 *             comment line before.
 	 */
-	public void setAction(Action newAction) {
+	public void setAction(Action newAction) throws IllegalTodoFileModification {
 		if (!Action.COMMENT.equals(action) && Action.COMMENT.equals(newAction)) {
 			// transforming from non-comment to comment
 			if (comment == null)
@@ -180,7 +183,7 @@ public class RebaseTodoLine {
 		} else if (Action.COMMENT.equals(action) && !Action.COMMENT.equals(newAction)) {
 			// transforming from comment to non-comment
 			if (commit == null)
-				throw new JGitInternalException(MessageFormat.format(
+				throw new IllegalTodoFileModification(MessageFormat.format(
 						JGitText.get().cannotChangeActionOnComment, action,
 						newAction));
 		}
@@ -219,12 +222,11 @@ public class RebaseTodoLine {
 		throw createInvalidCommentException(newComment);
 	}
 
-	private static JGitInternalException createInvalidCommentException(
+	private static IllegalArgumentException createInvalidCommentException(
 			String newComment) {
-		IllegalArgumentException iae = new IllegalArgumentException(
+		return new IllegalArgumentException(
 				MessageFormat.format(
 				JGitText.get().argumentIsNotAValidCommentString, newComment));
-		return new JGitInternalException(iae.getMessage(), iae);
 	}
 
 	/**