diff --git a/PBChangedFile.h b/PBChangedFile.h
index 0c68e81..73ee3f0 100644
--- a/PBChangedFile.h
+++ b/PBChangedFile.h
@@ -17,7 +17,8 @@ typedef enum {
 
 @interface PBChangedFile : NSObject {
 	NSString *path;
-	BOOL cached;
+	BOOL hasCachedChanges;
+	BOOL hasUnstagedChanges;
 	__weak PBGitRepository *repository;
 	PBChangedFileStatus status;
 }
@@ -25,7 +26,8 @@ typedef enum {
 
 @property (readonly) NSString *path;
 @property (assign) PBChangedFileStatus status;
-@property (assign) BOOL cached;
+@property (assign) BOOL hasCachedChanges;
+@property (assign) BOOL hasUnstagedChanges;
 - (NSImage *)icon;
 - (NSString *)changes;
 - (void) stageChanges;
diff --git a/PBChangedFile.m b/PBChangedFile.m
index 518ca64..3bb0ae7 100644
--- a/PBChangedFile.m
+++ b/PBChangedFile.m
@@ -11,7 +11,7 @@
 
 @implementation PBChangedFile
 
-@synthesize path, status, cached;
+@synthesize path, status, hasCachedChanges, hasUnstagedChanges;
 
 - (id) initWithPath:(NSString *)p andRepository:(PBGitRepository *)r
 {
@@ -20,18 +20,20 @@
 	return self;
 }
 
-- (NSString *) changes
+- (NSString *) cachedChanges
+{
+	return [repository outputInWorkdirForArguments:[NSArray arrayWithObjects:@"diff", @"--cached", @"--", path, nil]];
+}
+
+- (NSString *)unstagedChanges
 {
 	if (status == NEW)
 		return [PBEasyPipe outputForCommand:@"/bin/cat" withArgs:[NSArray arrayWithObject:path] inDir:[repository workingDirectory]];
-	else {
-		if (cached == YES)
-			return [repository outputInWorkdirForArguments:[NSArray arrayWithObjects:@"diff", @"--cached", @"--", path, nil]];
-		else
-			return [repository outputInWorkdirForArguments:[NSArray arrayWithObjects:@"diff", @"--", path, nil]];
-	}
+
+	return [repository outputInWorkdirForArguments:[NSArray arrayWithObjects:@"diff", @"--", path, nil]];
 }
 
+
 - (NSImage *) icon
 {
 	NSString *filename;
@@ -57,12 +59,15 @@
 	else
 		[repository outputInWorkdirForArguments:[NSArray arrayWithObjects:@"add", path, nil]];
 
-	self.cached = YES;
+	self.hasUnstagedChanges = NO;
+	self.hasCachedChanges = YES;
 }
+
 - (void) unstageChanges
 {
 	[repository outputInWorkdirForArguments:[NSArray arrayWithObjects:@"reset", @"--", path, nil]];
-	self.cached = NO;
+	self.hasCachedChanges = NO;
+	self.hasUnstagedChanges = YES;
 }
 
 + (BOOL)isSelectorExcludedFromWebScript:(SEL)aSelector
diff --git a/PBGitCommitController.m b/PBGitCommitController.m
index 502ce7e..b6d5e2a 100644
--- a/PBGitCommitController.m
+++ b/PBGitCommitController.m
@@ -29,8 +29,8 @@
 
 	[commitMessageView setTypingAttributes:[NSDictionary dictionaryWithObject:[NSFont fontWithName:@"Monaco" size:12.0] forKey:NSFontAttributeName]];
 	
-	[unstagedFilesController setFilterPredicate:[NSPredicate predicateWithFormat:@"cached == 0"]];
-	[cachedFilesController setFilterPredicate:[NSPredicate predicateWithFormat:@"cached == 1"]];
+	[unstagedFilesController setFilterPredicate:[NSPredicate predicateWithFormat:@"hasUnstagedChanges == 1"]];
+	[cachedFilesController setFilterPredicate:[NSPredicate predicateWithFormat:@"hasCachedChanges == 1"]];
 	
 	[unstagedFilesController setSortDescriptors:[NSArray arrayWithObjects:
 		[[NSSortDescriptor alloc] initWithKey:@"status" ascending:false],
@@ -110,6 +110,8 @@
 {
 	if (!--self.busy)
 		self.status = @"Ready";
+	[unstagedFilesController didChangeArrangementCriteria];
+	[cachedFilesController didChangeArrangementCriteria];
 }
 
 - (void) readOtherFiles:(NSNotification *)notification;
@@ -120,15 +122,16 @@
 			continue;
 		PBChangedFile *file =[[PBChangedFile alloc] initWithPath:line andRepository:repository];
 		file.status = NEW;
-		file.cached = NO;
-		[unstagedFilesController addObject:file];
+		file.hasCachedChanges = NO;
+		file.hasUnstagedChanges = YES;
+
+		[files addObject: file];
 	}
 	[self doneProcessingIndex];
 }
 
-- (void) readUnstagedFiles:(NSNotification *)notification
+- (void) addFilesFromLines:(NSArray *)lines cached:(BOOL) cached
 {
-	NSArray *lines = [self linesFromNotification:notification];
 	NSArray *fileStatus;
 	int even = 0;
 	for (NSString *line in lines) {
@@ -138,54 +141,44 @@
 			continue;
 		}
 		even = 0;
-		
+
+		// If the file is already added, we shouldn't add it again
+		// but rather update it to incorporate our changes
+		NSArray *existingFiles = [files filteredArrayUsingPredicate:[NSPredicate predicateWithFormat:@"path == '%@'", line]];
+		if ([existingFiles count] != 0) {
+			PBChangedFile *file = [existingFiles objectAtIndex:0];
+			if (cached)
+				file.hasCachedChanges = YES;
+			else
+				file.hasUnstagedChanges = YES;
+			return;
+		}
+
 		PBChangedFile *file = [[PBChangedFile alloc] initWithPath:line andRepository:repository];
 		if ([[fileStatus objectAtIndex:4] isEqualToString:@"D"])
 			file.status = DELETED;
 		else
 			file.status = MODIFIED;
 
-		file.cached = NO;
+		file.hasCachedChanges = cached;
+		file.hasUnstagedChanges = !cached;
 
-		// FIXME: If you are in a merge and have conflicts, a file is displayed twice, with different
-		// index values. For now, we don't handle this gracefully.
-		BOOL fileExists = NO;
-		for (PBChangedFile *object in [unstagedFilesController arrangedObjects]) {
-			if ([[object path] isEqualToString:[file path]]) {
-				fileExists = YES;
-				break;
-			}
-		}
-		if (!fileExists)
-			[unstagedFilesController addObject: file];
+		[files addObject: file];
 	}
+
+}
+
+- (void) readUnstagedFiles:(NSNotification *)notification
+{
+	NSArray *lines = [self linesFromNotification:notification];
+	[self addFilesFromLines:lines cached:NO];
 	[self doneProcessingIndex];
 }
 
 - (void) readCachedFiles:(NSNotification *)notification
 {
 	NSArray *lines = [self linesFromNotification:notification];
-	NSLog(@"Reading cached files!");
-	NSArray *fileStatus;
-	int even = 0;
-	for (NSString *line in lines) {
-		if (!even) {
-			even = 1;
-			fileStatus = [line componentsSeparatedByString:@" "];
-			continue;
-		}
-		even = 0;
-		
-		PBChangedFile *file = [[PBChangedFile alloc] initWithPath:line andRepository:repository];
-		if ([[fileStatus objectAtIndex:4] isEqualToString:@"D"])
-			file.status = DELETED;
-		else
-			file.status = MODIFIED;
-		
-		file.cached = YES;
-		[cachedFilesController addObject: file];
-	}
-	self.files = files;
+	[self addFilesFromLines:lines cached:YES];
 	[self doneProcessingIndex];
 }
 
@@ -284,7 +277,7 @@
 	
 	PBChangedFile *selectedItem = [[controller arrangedObjects] objectAtIndex:selectionIndex];
 	[controller removeObject:selectedItem];
-	if (selectedItem.cached == NO)
+	if ([tableView tag] == 0)
 		[selectedItem stageChanges];
 	else
 		[selectedItem unstageChanges];
diff --git a/PBWebChangesController.h b/PBWebChangesController.h
index e3b2ac5..de934cc 100644
--- a/PBWebChangesController.h
+++ b/PBWebChangesController.h
@@ -19,5 +19,5 @@
 	id previousFile;
 }
 
-- (void) showDiff:(PBChangedFile *)file;
+- (void) showDiff:(PBChangedFile *)file cached:(BOOL)cached;
 @end
diff --git a/PBWebChangesController.m b/PBWebChangesController.m
index ca7ae8b..12dd72f 100644
--- a/PBWebChangesController.m
+++ b/PBWebChangesController.m
@@ -24,7 +24,7 @@ static PBChangedFile *lastFileSelected = nil;
 - (void) didLoad
 {
 	if (lastFileSelected)
-		[self showDiff: lastFileSelected];
+		[self showDiff: lastFileSelected cached:NO];
 }
 
 - (void)observeValueForKeyPath:(NSString *)keyPath
@@ -35,6 +35,7 @@ static PBChangedFile *lastFileSelected = nil;
 	if ([[object selectedObjects] count] == 0)
 		return;
 
+	// TODO: Move this to commitcontroller
 	if (object == unstagedFilesController)
 		[cachedFilesController setSelectionIndexes:[NSIndexSet indexSet]];
 	else
@@ -42,10 +43,10 @@ static PBChangedFile *lastFileSelected = nil;
 
 	PBChangedFile *file = [[object selectedObjects] objectAtIndex:0];
 
-	[self showDiff: file];
+	[self showDiff: file cached: object == cachedFilesController];
 }
 
-- (void) showDiff:(PBChangedFile *)file
+- (void) showDiff:(PBChangedFile *)file cached:(BOOL) cached
 {
 	if (!finishedLoading) {
 		lastFileSelected = file;
@@ -59,6 +60,7 @@ static PBChangedFile *lastFileSelected = nil;
 	previousFile = file;
 
 	id script = [view windowScriptObject];
-	[script callWebScriptMethod:@"showFileChanges" withArguments:[NSArray arrayWithObject:file]];	
+	NSLog(@"Showing diff..");
+	[script callWebScriptMethod:@"showFileChanges" withArguments:[NSArray arrayWithObjects:file, [NSNumber numberWithBool:cached], nil]];
 }
 @end
diff --git a/html/diff.html b/html/diff.html
index f346578..47ceb5a 100644
--- a/html/diff.html
+++ b/html/diff.html
@@ -7,11 +7,11 @@
 	<script src="commit.js" type="text/javascript" charset="utf-8"></script>
 	<script src="diff.js" type="text/javascript" charset="utf-8"></script>
 	<script>
-		var showFileChanges = function(file) {
+		var showFileChanges = function(file, cached) {
 			// New file?
 			if (file.status == 0)
 			{
-				var contents = file.changes();
+				var contents = file.unstagedChanges();
 				if (contents)
 					$("diff").innerHTML = contents.escapeHTML();
 				else
@@ -21,7 +21,10 @@
 				$('title').innerHTML = "New file: " + file.path;
 			}  else {
 				$("diff").hide();
-				$("diff").innerHTML = file.changes().escapeHTML();
+				if (cached)
+					$("diff").innerHTML = file.cachedChanges().escapeHTML();
+				else
+					$("diff").innerHTML = file.unstagedChanges().escapeHTML();
 				highlightDiffs();
 				$("diff").show();
 				$("title").innerHTML = "Changes for " + file.path;