diff --git a/GitX.xcodeproj/project.pbxproj b/GitX.xcodeproj/project.pbxproj
index be97512..d091d92 100644
--- a/GitX.xcodeproj/project.pbxproj
+++ b/GitX.xcodeproj/project.pbxproj
@@ -97,6 +97,7 @@
 		F59116E90E843BCB0072CCB1 /* PBGitCommitController.m in Sources */ = {isa = PBXBuildFile; fileRef = F59116E80E843BCB0072CCB1 /* PBGitCommitController.m */; };
 		F593DF780E9E636C003A8559 /* PBFileChangesTableView.m in Sources */ = {isa = PBXBuildFile; fileRef = F593DF770E9E636C003A8559 /* PBFileChangesTableView.m */; };
 		F5945E170E02B0C200706420 /* PBGitRepository.m in Sources */ = {isa = PBXBuildFile; fileRef = F5945E160E02B0C200706420 /* PBGitRepository.m */; };
+		F59F1DD5105C4FF300115F88 /* PBGitIndex.m in Sources */ = {isa = PBXBuildFile; fileRef = F59F1DD4105C4FF300115F88 /* PBGitIndex.m */; };
 		F5AD56790E79B78100EDAAFE /* PBCommitList.m in Sources */ = {isa = PBXBuildFile; fileRef = F5AD56780E79B78100EDAAFE /* PBCommitList.m */; };
 		F5B721C40E05CF7E00AF29DC /* MainMenu.xib in Resources */ = {isa = PBXBuildFile; fileRef = F5B721C20E05CF7E00AF29DC /* MainMenu.xib */; };
 		F5C007750E731B48007B84B2 /* PBGitRef.m in Sources */ = {isa = PBXBuildFile; fileRef = F5C007740E731B48007B84B2 /* PBGitRef.m */; };
@@ -250,6 +251,8 @@
 		F593DF770E9E636C003A8559 /* PBFileChangesTableView.m */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.objc; path = PBFileChangesTableView.m; sourceTree = "<group>"; };
 		F5945E150E02B0C200706420 /* PBGitRepository.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = PBGitRepository.h; sourceTree = "<group>"; };
 		F5945E160E02B0C200706420 /* PBGitRepository.m */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.objc; path = PBGitRepository.m; sourceTree = "<group>"; };
+		F59F1DD3105C4FF300115F88 /* PBGitIndex.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = PBGitIndex.h; sourceTree = "<group>"; };
+		F59F1DD4105C4FF300115F88 /* PBGitIndex.m */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.objc; path = PBGitIndex.m; sourceTree = "<group>"; };
 		F5AD56770E79B78100EDAAFE /* PBCommitList.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = PBCommitList.h; sourceTree = "<group>"; };
 		F5AD56780E79B78100EDAAFE /* PBCommitList.m */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.objc; path = PBCommitList.m; sourceTree = "<group>"; };
 		F5B721C30E05CF7E00AF29DC /* English */ = {isa = PBXFileReference; lastKnownFileType = file.xib; name = English; path = English.lproj/MainMenu.xib; sourceTree = "<group>"; };
@@ -467,6 +470,7 @@
 		F56174540E05887E001DCD79 /* Git */ = {
 			isa = PBXGroup;
 			children = (
+				F59F1DD2105C4FDE00115F88 /* Index */,
 				F5E927E30E883D6800056E75 /* Commit */,
 				F5E927E10E883D2E00056E75 /* History */,
 				F5945E150E02B0C200706420 /* PBGitRepository.h */,
@@ -549,6 +553,17 @@
 			name = SpeedTest;
 			sourceTree = "<group>";
 		};
+		F59F1DD2105C4FDE00115F88 /* Index */ = {
+			isa = PBXGroup;
+			children = (
+				F5E927F60E883E7200056E75 /* PBChangedFile.h */,
+				F5E927F70E883E7200056E75 /* PBChangedFile.m */,
+				F59F1DD3105C4FF300115F88 /* PBGitIndex.h */,
+				F59F1DD4105C4FF300115F88 /* PBGitIndex.m */,
+			);
+			name = Index;
+			sourceTree = "<group>";
+		};
 		F5B161BB0EAB6E0C005A1DE1 /* Diff */ = {
 			isa = PBXGroup;
 			children = (
@@ -604,8 +619,6 @@
 			children = (
 				93F7857D0EA3ABF100C1F443 /* PBCommitMessageView.h */,
 				93F7857E0EA3ABF100C1F443 /* PBCommitMessageView.m */,
-				F5E927F60E883E7200056E75 /* PBChangedFile.h */,
-				F5E927F70E883E7200056E75 /* PBChangedFile.m */,
 				F593DF760E9E636C003A8559 /* PBFileChangesTableView.h */,
 				F593DF770E9E636C003A8559 /* PBFileChangesTableView.m */,
 			);
@@ -854,6 +867,7 @@
 				47DBDBCA0E95016F00671A1E /* PBNSURLPathUserDefaultsTransfomer.m in Sources */,
 				F562C8870FE1766C000EC528 /* NSString_RegEx.m in Sources */,
 				EB2A734A0FEE3F09006601CF /* PBCollapsibleSplitView.m in Sources */,
+				F59F1DD5105C4FF300115F88 /* PBGitIndex.m in Sources */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
 		};
diff --git a/PBGitIndex.h b/PBGitIndex.h
new file mode 100644
index 0000000..9fc784e
--- /dev/null
+++ b/PBGitIndex.h
@@ -0,0 +1,52 @@
+//
+//  PBGitIndex.h
+//  GitX
+//
+//  Created by Pieter de Bie on 9/12/09.
+//  Copyright 2009 Pieter de Bie. All rights reserved.
+//
+
+#import <Cocoa/Cocoa.h>
+
+@class PBGitRepository;
+
+// Represents a git index for a given work tree.
+// As a single git repository can have multiple trees,
+// the tree has to be given explicitly, even though
+// multiple trees is not yet supported in GitX
+@interface PBGitIndex : NSObject {
+	
+@private
+	PBGitRepository *repository;
+	NSURL *workingDirectory;
+	NSMutableArray *files;
+
+	NSUInteger refreshStatus;
+	NSDictionary *amendEnvironment;
+	BOOL amend;
+}
+
+// Whether we want the changes for amending,
+// or for
+@property BOOL amend;
+
+- (id)initWithRepository:(PBGitRepository *)repository workingDirectory:(NSURL *)workingDirectory;
+
+// A list of PBChangedFile's with differences between the work tree and the index
+// This method is KVO-aware, so changes when any of the index-modifying methods are called
+// (including -refresh)
+- (NSArray *)indexChanges;
+
+// Refresh the index
+- (void)refresh;
+
+//- (void)commit;
+
+// Inter-file changes:
+//- (void)stageFiles:(NSArray *)files;
+//- (void)unstageFiles:(NSArray *)files;
+
+// Intra-file changes
+//- (void)applyPatch:(NSString *)hunk stage:(BOOL)stage reverse:(BOOL)reverse;
+
+@end
diff --git a/PBGitIndex.m b/PBGitIndex.m
new file mode 100644
index 0000000..29e9ff8
--- /dev/null
+++ b/PBGitIndex.m
@@ -0,0 +1,345 @@
+//
+//  PBGitIndex.m
+//  GitX
+//
+//  Created by Pieter de Bie on 9/12/09.
+//  Copyright 2009 Pieter de Bie. All rights reserved.
+//
+
+#import "PBGitIndex.h"
+#import "PBGitRepository.h"
+#import "PBGitBinary.h"
+#import "PBEasyPipe.h"
+#import "NSString_RegEx.h"
+#import "PBChangedFile.h"
+
+@interface PBGitIndex (IndexRefreshMethods)
+
+- (NSArray *)linesFromNotification:(NSNotification *)notification;
+- (NSMutableDictionary *)dictionaryForLines:(NSArray *)lines;
+- (void)addFilesFromDictionary:(NSMutableDictionary *)dictionary staged:(BOOL)staged tracked:(BOOL)tracked;
+
+- (void)indexStepComplete;
+
+- (void)indexRefreshFinished:(NSNotification *)notification;
+- (void)readOtherFiles:(NSNotification *)notification;
+- (void)readUnstagedFiles:(NSNotification *)notification;
+- (void)readStagedFiles:(NSNotification *)notification;
+
+@end
+
+@interface PBGitIndex ()
+
+// Returns the tree to compare the index to, based
+// on whether amend is set or not.
+- (NSString *) parentTree;
+
+@end
+
+@implementation PBGitIndex
+
+@synthesize amend;
+
+- (id)initWithRepository:(PBGitRepository *)theRepository workingDirectory:(NSURL *)theWorkingDirectory
+{
+	if (!(self = [super init]))
+		return nil;
+
+	NSAssert(theWorkingDirectory, @"PBGitIndex requires a working directory");
+	NSAssert(theRepository, @"PBGitIndex requires a repository");
+
+	repository = theRepository;
+	workingDirectory = theWorkingDirectory;
+	files = [NSMutableArray array];
+
+	return self;
+}
+
+- (NSArray *)indexChanges
+{
+	return files;
+}
+
+- (void)setAmend:(BOOL)newAmend
+{
+	if (newAmend == amend)
+		return;
+	
+	amend = newAmend;
+	amendEnvironment = nil;
+
+	[self refresh];
+
+	if (!newAmend)
+		return;
+
+	// If we amend, we want to keep the author information for the previous commit
+	// We do this by reading in the previous commit, and storing the information
+	// in a dictionary. This dictionary will then later be read by [self commit:]
+	NSString *message = [repository outputForCommand:@"cat-file commit HEAD"];
+	NSArray *match = [message substringsMatchingRegularExpression:@"\nauthor ([^\n]*) <([^\n>]*)> ([0-9]+[^\n]*)\n" count:3 options:0 ranges:nil error:nil];
+	if (match)
+		amendEnvironment = [NSDictionary dictionaryWithObjectsAndKeys:[match objectAtIndex:1], @"GIT_AUTHOR_NAME",
+							[match objectAtIndex:2], @"GIT_AUTHOR_EMAIL",
+							[match objectAtIndex:3], @"GIT_AUTHOR_DATE",
+							nil];
+}
+
+- (void)refresh
+{
+	// If we were already refreshing the index, we don't want
+	// double notifications. As we can't stop the tasks anymore,
+	// just cancel the notifications
+	refreshStatus = 0;
+	NSNotificationCenter *nc = [NSNotificationCenter defaultCenter]; 
+	[nc removeObserver:self]; 
+
+	// Ask Git to refresh the index
+	NSFileHandle *updateHandle = [PBEasyPipe handleForCommand:[PBGitBinary path] 
+													 withArgs:[NSArray arrayWithObjects:@"update-index", @"-q", @"--unmerged", @"--ignore-missing", @"--refresh", nil]
+														inDir:[workingDirectory path]];
+
+	[nc addObserver:self
+		   selector:@selector(indexRefreshFinished:)
+			   name:NSFileHandleReadToEndOfFileCompletionNotification
+			 object:updateHandle];
+	[updateHandle readToEndOfFileInBackgroundAndNotify];
+
+}
+
+- (NSString *) parentTree
+{
+	NSString *parent = amend ? @"HEAD^" : @"HEAD";
+	
+	if (![repository parseReference:parent])
+		// We don't have a head ref. Return the empty tree.
+		return @"4b825dc642cb6eb9a060e54bf8d69288fbee4904";
+
+	return parent;
+}
+
+@end
+
+@implementation PBGitIndex (IndexRefreshMethods)
+
+- (void)indexRefreshFinished:(NSNotification *)notification
+{
+	if ([(NSNumber *)[(NSDictionary *)[notification userInfo] objectForKey:@"NSFileHandleError"] intValue])
+	{
+		// TODO: send updatefailed notification?
+		return;
+	}
+
+	// Now that the index is refreshed, we need to read the information from the index
+	NSNotificationCenter *nc = [NSNotificationCenter defaultCenter]; 
+
+	// Other files (not tracked, not ignored)
+	NSFileHandle *handle = [PBEasyPipe handleForCommand:[PBGitBinary path] 
+											   withArgs:[NSArray arrayWithObjects:@"ls-files", @"--others", @"--exclude-standard", @"-z", nil]
+												  inDir:[workingDirectory path]];
+	[nc addObserver:self selector:@selector(readOtherFiles:) name:NSFileHandleReadToEndOfFileCompletionNotification object:handle]; 
+	[handle readToEndOfFileInBackgroundAndNotify];
+	refreshStatus++;
+
+	// Unstaged files
+	handle = [PBEasyPipe handleForCommand:[PBGitBinary path] 
+											   withArgs:[NSArray arrayWithObjects:@"diff-files", @"-z", nil]
+												  inDir:[workingDirectory path]];
+	[nc addObserver:self selector:@selector(readUnstagedFiles:) name:NSFileHandleReadToEndOfFileCompletionNotification object:handle]; 
+	[handle readToEndOfFileInBackgroundAndNotify];
+	refreshStatus++;
+
+	// Staged files
+	handle = [PBEasyPipe handleForCommand:[PBGitBinary path] 
+								 withArgs:[NSArray arrayWithObjects:@"diff-index", @"--cached", @"-z", [self parentTree], nil]
+									inDir:[workingDirectory path]];
+	[nc addObserver:self selector:@selector(readStagedFiles:) name:NSFileHandleReadToEndOfFileCompletionNotification object:handle]; 
+	[handle readToEndOfFileInBackgroundAndNotify];
+	refreshStatus++;
+}
+
+- (void)readOtherFiles:(NSNotification *)notification
+{
+	NSArray *lines = [self linesFromNotification:notification];
+	NSMutableDictionary *dictionary = [[NSMutableDictionary alloc] initWithCapacity:[lines count]];
+	// Other files are untracked, so we don't have any real index information. Instead, we can just fake it.
+	// The line below is used to add the file to the index
+	// FIXME: request the real file mode
+	NSArray *fileStatus = [NSArray arrayWithObjects:@":000000", @"100644", @"0000000000000000000000000000000000000000", @"0000000000000000000000000000000000000000", @"A", nil];
+	for (NSString *path in lines) {
+		if ([path length] == 0)
+			continue;
+		[dictionary setObject:fileStatus forKey:path];
+	}
+
+	[self addFilesFromDictionary:dictionary staged:NO tracked:NO];
+	[self indexStepComplete];	
+}
+
+- (void) readStagedFiles:(NSNotification *)notification
+{
+	NSArray *lines = [self linesFromNotification:notification];
+	NSMutableDictionary *dic = [self dictionaryForLines:lines];
+	[self addFilesFromDictionary:dic staged:YES tracked:YES];
+	[self indexStepComplete];
+}
+
+- (void) readUnstagedFiles:(NSNotification *)notification
+{
+	NSArray *lines = [self linesFromNotification:notification];
+	NSMutableDictionary *dic = [self dictionaryForLines:lines];
+	[self addFilesFromDictionary:dic staged:NO tracked:YES];
+	[self indexStepComplete];
+}
+
+- (void) addFilesFromDictionary:(NSMutableDictionary *)dictionary staged:(BOOL)staged tracked:(BOOL)tracked
+{
+	// TODO: Stop tracking files
+	// Iterate over all existing files
+	for (PBChangedFile *file in files) {
+		NSArray *fileStatus = [dictionary objectForKey:file.path];
+		// Object found, this is still a cached / uncached thing
+		if (fileStatus) {
+			if (tracked) {
+				NSString *mode = [[fileStatus objectAtIndex:0] substringFromIndex:1];
+				NSString *sha = [fileStatus objectAtIndex:2];
+				file.commitBlobSHA = sha;
+				file.commitBlobMode = mode;
+				
+				if (staged)
+					file.hasStagedChanges = YES;
+				else
+					file.hasUnstagedChanges = YES;
+			} else {
+				// Untracked file, set status to NEW, only unstaged changes
+				file.hasStagedChanges = NO;
+				file.hasUnstagedChanges = YES;
+				file.status = NEW;
+			}
+
+			// We handled this file, remove it from the dictionary
+			[dictionary removeObjectForKey:file.path];
+		} else {
+			// Object not found in the dictionary, so let's reset its appropriate
+			// change (stage or untracked) if necessary.
+
+			// Staged dictionary, so file does not have staged changes
+			if (staged)
+				file.hasStagedChanges = NO;
+			// Tracked file does not have unstaged changes, file is not new,
+			// so we can set it to No. (If it would be new, it would not
+			// be in this dictionary, but in the "other dictionary").
+			else if (tracked && file.status != NEW)
+				file.hasUnstagedChanges = NO;
+			// Unstaged, untracked dictionary ("Other" files), and file
+			// is indicated as new (which would be untracked), so let's
+			// remove it
+			else if (!tracked && file.status == NEW)
+				file.hasUnstagedChanges = NO;
+		}
+	}
+	// TODO: Finish tracking files
+
+	// Do new files only if necessary
+	if (![[dictionary allKeys] count])
+		return;
+
+	// All entries left in the dictionary haven't been accounted for
+	// above, so we need to add them to the "files" array
+	[self willChangeValueForKey:@"indexChanges"];
+	for (NSString *path in [dictionary allKeys]) {
+		NSArray *fileStatus = [dictionary objectForKey:path];
+
+		PBChangedFile *file = [[PBChangedFile alloc] initWithPath:path];
+		if ([[fileStatus objectAtIndex:4] isEqualToString:@"D"])
+			file.status = DELETED;
+		else if([[fileStatus objectAtIndex:0] isEqualToString:@":000000"])
+			file.status = NEW;
+		else
+			file.status = MODIFIED;
+
+		if (tracked) {
+			file.commitBlobMode = [[fileStatus objectAtIndex:0] substringFromIndex:1];
+			file.commitBlobSHA = [fileStatus objectAtIndex:2];
+		}
+
+		file.hasStagedChanges = staged;
+		file.hasUnstagedChanges = !staged;
+
+		[files addObject:file];
+	}
+	[self didChangeValueForKey:@"indexChanges"];
+}
+
+# pragma mark Utility methods
+- (NSArray *)linesFromNotification:(NSNotification *)notification
+{
+	NSData *data = [[notification userInfo] valueForKey:NSFileHandleNotificationDataItem];
+	if (!data)
+		return [NSArray array];
+
+	NSString *string = [[NSString alloc] initWithData:data encoding:NSUTF8StringEncoding];
+	// FIXME: Return an error?
+	if (!string)
+		return [NSArray array];
+
+	// Strip trailing null
+	if ([string hasSuffix:@"\0"])
+		string = [string substringToIndex:[string length]-1];
+
+	if ([string length] == 0)
+		return [NSArray array];
+
+	return [string componentsSeparatedByString:@"\0"];
+}
+
+- (NSMutableDictionary *)dictionaryForLines:(NSArray *)lines
+{
+	NSMutableDictionary *dictionary = [NSMutableDictionary dictionaryWithCapacity:[lines count]/2];
+	
+	// Fill the dictionary with the new information. These lines are in the form of:
+	// :00000 :0644 OTHER INDEX INFORMATION
+	// Filename
+
+	NSAssert1([lines count] % 2 == 0, @"Lines must have an even number of lines: %@", lines);
+
+	NSEnumerator *enumerator = [lines objectEnumerator];
+	NSString *fileStatus;
+	while (fileStatus = [enumerator nextObject]) {
+		NSString *fileName = [enumerator nextObject];
+		[dictionary setObject:[fileStatus componentsSeparatedByString:@" "] forKey:fileName];
+	}
+
+	return dictionary;
+}
+
+// This method is called for each of the three processes from above.
+// If all three are finished (self.busy == 0), then we can delete
+// all files previously marked as deletable
+- (void)indexStepComplete
+{
+	// if we're still busy, do nothing :)
+	if (--refreshStatus)
+		return;
+
+	// At this point, all index operations have finished.
+	// We need to find all files that don't have either
+	// staged or unstaged files, and delete them
+
+	NSMutableArray *deleteFiles = [NSMutableArray array];
+	for (PBChangedFile *file in files) {
+		if (!file.hasStagedChanges && !file.hasUnstagedChanges)
+			[deleteFiles addObject:file];
+	}
+	
+	if ([deleteFiles count]) {
+		[self willChangeValueForKey:@"indexChanges"];
+		for (PBChangedFile *file in deleteFiles)
+			[files removeObject:file];
+		[self didChangeValueForKey:@"indexChanges"];
+	}
+
+	// TODO: Sent index refresh finished operation
+}
+
+@end