Fix merge/cherry-picking in CRLF mode

This fixes a case where we have CRLF in the repo but
LF in the worktree and are in autocrlf mode.

Change-Id: I0388270c1cf0fd22dfd513bcaa404eb97268d39d
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/ResolveMergerTest.java

diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/ResolveMergerTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/ResolveMergerTest.java
index 54de8cf..dd06168 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/ResolveMergerTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/ResolveMergerTest.java
@@ -53,6 +53,7 @@
 import org.eclipse.jgit.api.MergeResult;
 import org.eclipse.jgit.api.MergeResult.MergeStatus;
 import org.eclipse.jgit.api.errors.CheckoutConflictException;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.errors.NoMergeBaseException;
@@ -264,6 +265,37 @@ public void checkUntrackedEmpytFolderIsNotAConflictWithFile(
 				indexState(CONTENT));
 	}
 
+	@Theory
+	public void mergeWithCrlfInWT(MergeStrategy strategy) throws IOException,
+			GitAPIException {
+		Git git = Git.wrap(db);
+		db.getConfig().setString("core", null, "autocrlf", "false");
+		db.getConfig().save();
+		writeTrashFile("crlf.txt", "some\r\ndata\r\n");
+		git.add().addFilepattern("crlf.txt").call();
+		git.commit().setMessage("base").call();
+
+		git.branchCreate().setName("brancha").call();
+
+		writeTrashFile("crlf.txt", "some\r\nmore\r\ndata\r\n");
+		git.add().addFilepattern("crlf.txt").call();
+		git.commit().setMessage("on master").call();
+
+		git.checkout().setName("brancha").call();
+		writeTrashFile("crlf.txt", "some\r\ndata\r\ntoo\r\n");
+		git.add().addFilepattern("crlf.txt").call();
+		git.commit().setMessage("on brancha").call();
+
+		db.getConfig().setString("core", null, "autocrlf", "input");
+		db.getConfig().save();
+
+		MergeResult mergeResult = git.merge().setStrategy(strategy)
+				.include(db.resolve("master"))
+				.call();
+		assertEquals(MergeResult.MergeStatus.MERGED,
+				mergeResult.getMergeStatus());
+	}
+
 	/**
 	 * Merging two equal subtrees when the index does not contain any file in
 	 * that subtree should lead to a merged state.

org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java

diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java b/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
index 414746d..a891c85 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
@@ -439,7 +439,7 @@ private boolean processEntry(CanonicalTreeParser base,
 					else {
 						// the preferred version THEIRS has a different mode
 						// than ours. Check it out!
-						if (isWorktreeDirty(work))
+						if (isWorktreeDirty(work, ourDce))
 							return false;
 						// we know about length and lastMod only after we have written the new content.
 						// This will happen later. Set these values to 0 for know.
@@ -477,7 +477,7 @@ private boolean processEntry(CanonicalTreeParser base,
 			// THEIRS. THEIRS is chosen.
 
 			// Check worktree before checking out THEIRS
-			if (isWorktreeDirty(work))
+			if (isWorktreeDirty(work, ourDce))
 				return false;
 			if (nonTree(modeT)) {
 				// we know about length and lastMod only after we have written
@@ -535,7 +535,7 @@ private boolean processEntry(CanonicalTreeParser base,
 
 		if (nonTree(modeO) && nonTree(modeT)) {
 			// Check worktree before modifying files
-			if (isWorktreeDirty(work))
+			if (isWorktreeDirty(work, ourDce))
 				return false;
 
 			// Don't attempt to resolve submodule link conflicts
@@ -566,7 +566,7 @@ private boolean processEntry(CanonicalTreeParser base,
 				// OURS was deleted checkout THEIRS
 				if (modeO == 0) {
 					// Check worktree before checking out THEIRS
-					if (isWorktreeDirty(work))
+					if (isWorktreeDirty(work, ourDce))
 						return false;
 					if (nonTree(modeT)) {
 						if (e != null)
@@ -625,7 +625,8 @@ private boolean isIndexDirty() {
 		return isDirty;
 	}
 
-	private boolean isWorktreeDirty(WorkingTreeIterator work) {
+	private boolean isWorktreeDirty(WorkingTreeIterator work,
+			DirCacheEntry ourDce) throws IOException {
 		if (work == null)
 			return false;
 
@@ -633,9 +634,15 @@ private boolean isWorktreeDirty(WorkingTreeIterator work) {
 		final int modeO = tw.getRawMode(T_OURS);
 
 		// Worktree entry has to match ours to be considered clean
-		boolean isDirty = work.isModeDifferent(modeO);
-		if (!isDirty && nonTree(modeF))
-			isDirty = !tw.idEqual(T_FILE, T_OURS);
+		boolean isDirty;
+		if (ourDce != null)
+			isDirty = work.isModified(ourDce, true, reader);
+		else {
+			isDirty = work.isModeDifferent(modeO);
+			if (!isDirty && nonTree(modeF))
+				isDirty = !tw.idEqual(T_FILE, T_OURS);
+		}
+
 		// Ignore existing empty directories
 		if (isDirty && modeF == FileMode.TYPE_TREE
 				&& modeO == FileMode.TYPE_MISSING)