PatchApplier fix - init cache with provided tree

This change only affects inCore repositories.
Before this change, any file that wasn't part of the patch
wasn't read, and therefore wasn't part of the output tree.

Change-Id: I246ef957088f17aaf367143f7a0b3af0f8264ffb
Bug: Google b/267270348

5 files changed, 83 insertions, 22 deletions

diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/Unaffected_PostImage b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/Unaffected_PostImage
new file mode 100644
index 0000000000..6b664d90c4
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/Unaffected_PostImage
@@ -0,0 +1,2 @@
+This file
+should not be changed.
\ No newline at end of file
diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/Unaffected_PreImage b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/Unaffected_PreImage
new file mode 100644
index 0000000000..6b664d90c4
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/Unaffected_PreImage
@@ -0,0 +1,2 @@
+This file
+should not be changed.
\ No newline at end of file
diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/XAndY.patch b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/XAndY.patch
new file mode 100644
index 0000000000..35950f3d08
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/XAndY.patch
@@ -0,0 +1,32 @@
+diff --git a/X b/X
+index a3648a1..2d44096 100644
+--- a/X
++++ b/X
+@@ -2,2 +2,3 @@ a
+ b
++c
+ d
+@@ -16,4 +17,2 @@ p
+ q
+-r
+-s
+ t
+@@ -22,4 +21,8 @@ v
+ w
+-x
+-y
++0
++1
++2
++3
++4
++5
+ z
+diff --git a/Y b/Y
+index 2e65efe..7898192 100644
+--- a/Y
++++ b/Y
+@@ -1 +1 @@
+-a
+\ No newline at end of file
++a
\ No newline at end of file
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/patch/PatchApplierTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/patch/PatchApplierTest.java
index bcde022d40..893fd61556 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/patch/PatchApplierTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/patch/PatchApplierTest.java
@@ -24,6 +24,7 @@ import java.io.InputStream;
 import java.io.OutputStream;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
+import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.errors.PatchApplyException;
 import org.eclipse.jgit.api.errors.PatchFormatException;
@@ -71,27 +72,21 @@ public class PatchApplierTest {
 			this.inCore = inCore;
 		}
 
+		void init(final String aName) throws Exception {
+			init(aName, true, true);
+		}
+
 		protected void init(String aName, boolean preExists, boolean postExists)
 				throws Exception {
 			// Patch and pre/postimage are read from data
 			// org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/
 			this.name = aName;
 			if (postExists) {
-				postImage = IO
-						.readWholeStream(getTestResource(name + "_PostImage"), 0)
-						.array();
-				expectedText = new String(postImage, StandardCharsets.UTF_8);
+				expectedText = initPostImage(aName);
 			}
 
-			File f = new File(db.getWorkTree(), name);
 			if (preExists) {
-				preImage = IO
-						.readWholeStream(getTestResource(name + "_PreImage"), 0)
-						.array();
-				try (Git git = new Git(db)) {
-					Files.write(f.toPath(), preImage);
-					git.add().addFilepattern(name).call();
-				}
+				initPreImage(aName);
 			}
 			try (Git git = new Git(db)) {
 				RevCommit base = git.commit().setMessage("PreImage").call();
@@ -99,8 +94,22 @@ public class PatchApplierTest {
 			}
 		}
 
-		void init(final String aName) throws Exception {
-			init(aName, true, true);
+		protected void initPreImage(String aName) throws Exception {
+			File f = new File(db.getWorkTree(), aName);
+			preImage = IO
+					.readWholeStream(getTestResource(aName + "_PreImage"), 0)
+					.array();
+			try (Git git = new Git(db)) {
+				Files.write(f.toPath(), preImage);
+				git.add().addFilepattern(aName).call();
+			}
+		}
+
+		protected String initPostImage(String aName) throws Exception {
+			postImage = IO
+					.readWholeStream(getTestResource(aName + "_PostImage"), 0)
+					.array();
+			return new String(postImage, StandardCharsets.UTF_8);
 		}
 
 		protected Result applyPatch()
@@ -118,27 +127,33 @@ public class PatchApplierTest {
 			return PatchApplierTest.class.getClassLoader()
 					.getResourceAsStream("org/eclipse/jgit/diff/" + patchFile);
 		}
+
 		void verifyChange(Result result, String aName) throws Exception {
 			verifyChange(result, aName, true);
 		}
 
 		protected void verifyContent(Result result, String path, boolean exists)
 				throws Exception {
+			verifyContent(result, path, exists ? expectedText : null);
+		}
+
+		protected void verifyContent(Result result, String path,
+				@Nullable String expectedContent) throws Exception {
 			if (inCore) {
 				byte[] output = readBlob(result.getTreeId(), path);
-				if (!exists)
+				if (expectedContent == null)
 					assertNull(output);
 				else {
 					assertNotNull(output);
-					assertEquals(expectedText,
+					assertEquals(expectedContent,
 							new String(output, StandardCharsets.UTF_8));
 				}
 			} else {
 				File f = new File(db.getWorkTree(), path);
-				if (!exists)
+				if (expectedContent == null)
 					assertFalse(f.exists());
 				else
-					checkFile(f, expectedText);
+					checkFile(f, expectedContent);
 			}
 		}
 
@@ -154,7 +169,7 @@ public class PatchApplierTest {
 					RevWalk rw = tr.getRevWalk()) {
 				db.incrementOpen();
 				RevTree tree = rw.parseTree(treeish);
-				try (TreeWalk tw = TreeWalk.forPath(db,path,tree)){
+				try (TreeWalk tw = TreeWalk.forPath(db, path, tree)) {
 					if (tw == null) {
 						return null;
 					}
@@ -300,7 +315,7 @@ public class PatchApplierTest {
 			assertTrue(result.getPaths().contains("RenameNoHunks"));
 			assertTrue(result.getPaths().contains("nested/subdir/Renamed"));
 
-			verifyContent(result,"nested/subdir/Renamed", true);
+			verifyContent(result, "nested/subdir/Renamed", true);
 		}
 
 		@Test
@@ -312,7 +327,7 @@ public class PatchApplierTest {
 			assertTrue(result.getPaths().contains("RenameWithHunks"));
 			assertTrue(result.getPaths().contains("nested/subdir/Renamed"));
 
-			verifyContent(result,"nested/subdir/Renamed", true);
+			verifyContent(result, "nested/subdir/Renamed", true);
 		}
 
 		@Test
@@ -355,6 +370,16 @@ public class PatchApplierTest {
 			verifyChange(result, "ShiftDown2");
 		}
 
+		@Test
+		public void testDoesNotAffectUnrelatedFiles() throws Exception {
+			initPreImage("Unaffected");
+			String expectedUnaffectedText = initPostImage("Unaffected");
+			init("X");
+
+			Result result = applyPatch();
+			verifyChange(result, "X");
+			verifyContent(result, "Unaffected", expectedUnaffectedText);
+		}
 	}
 
 	public static class InCore extends Base {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/patch/PatchApplier.java b/org.eclipse.jgit/src/org/eclipse/jgit/patch/PatchApplier.java
index 2a4de1331d..98a2804ee4 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/patch/PatchApplier.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/patch/PatchApplier.java
@@ -194,7 +194,7 @@ public class PatchApplier {
 				throw new PatchFormatException(p.getErrors());
 			}
 
-			DirCache dirCache = (inCore()) ? DirCache.newInCore()
+			DirCache dirCache = inCore() ? DirCache.read(reader, beforeTree)
 					: repo.lockDirCache();
 
 			DirCacheBuilder dirCacheBuilder = dirCache.builder();