Kind of starting from scratch.

Recreated the project as an xcode 4 project.
Key Bindings are working and reloading.
Got rid of everything that wasn't being used right now.

Atom/Classes/AtomApp.h

@@ -0,0 +1,12 @@
+#import <Cocoa/Cocoa.h>
+
+@class AtomController;
+
+@interface AtomApp : NSApplication <NSApplicationDelegate>
+
+@property (nonatomic, retain) NSMutableArray *controllers;
+
+- (AtomController *)createController;
+- (void)removeController:(AtomController *)controller;
+
+@end

Atom/Classes/AtomApp.m

@@ -0,0 +1,48 @@
+#import "AtomApp.h"
+#import "AtomController.h"
+#import "JSCocoa.h"
+
+@implementation AtomApp
+
+@synthesize controllers;
+
+- (AtomController *)createController {
+  AtomController *controller = [[AtomController alloc] initWithWindowNibName:@"AtomWindow"];
+  [controllers addObject:controller];
+  return controller;
+}
+
+- (void)removeController:(AtomController *)controller {
+  [controllers removeObject:controller];
+}
+
+// Overridden
+- (void)sendEvent:(NSEvent *)event {
+  if ([event type] == NSKeyDown) {
+    BOOL handeled = NO;
+    id controller = [[self keyWindow] windowController];
+    
+    // The keyWindow could be a Cocoa Dialog or something, ignore that.
+    if ([controller isKindOfClass:[AtomController class]]) {
+      handeled = [controller handleKeyEvent:event];
+    }
+    
+    if (!handeled) [super sendEvent:event];
+  }
+  else {
+    [super sendEvent:event];
+  }
+}
+
+// AppDelegate
+- (void)applicationWillFinishLaunching:(NSNotification *)aNotification {
+  NSDictionary *defaults = [NSDictionary dictionaryWithObjectsAndKeys:[NSNumber numberWithBool:YES], @"WebKitDeveloperExtras", nil];
+  [[NSUserDefaults standardUserDefaults] registerDefaults:defaults];
+}
+
+- (void)applicationDidFinishLaunching:(NSNotification *)aNotification {
+  AtomController *controller = [self createController];
+  [controller window];
+}
+
+@end

Atom/Classes/AtomController.h

@@ -0,0 +1,16 @@
+#import <Cocoa/Cocoa.h>
+
+@class JSCocoa;
+
+@interface AtomController : NSWindowController {
+  IBOutlet id webView;
+  NSString *URL;
+  JSCocoa* jscocoa;
+}
+
+@property (assign) IBOutlet id webView;
+@property (assign) IBOutlet NSString *URL;
+
+-(BOOL) handleKeyEvent:(NSEvent *)event;
+
+@end

Atom/Classes/AtomController.m

@@ -0,0 +1,67 @@
+#import "AtomController.h"
+#import "AtomApp.h"
+
+#import <WebKit/WebKit.h>
+#import "JSCocoa.h"
+
+@implementation AtomController
+
+@synthesize webView, URL;
+
+- (void)dealloc {
+  [jscocoa unlinkAllReferences];
+  [jscocoa garbageCollect];
+  [jscocoa release]; jscocoa = nil;
+
+  [webView release];
+  [URL release];
+
+  [super dealloc];
+}
+
+- (id)initWithURL:(NSString *)_URL {
+  self = [super initWithWindowNibName:@"AtomWindow"];
+  self.URL = _URL;
+  return self;
+}
+
+- (void)windowDidLoad {
+  [super windowDidLoad];
+
+  [webView setUIDelegate:self];
+
+  [self setShouldCascadeWindows:YES];
+  [self setWindowFrameAutosaveName:@"atomController"];
+
+  if (self.URL) {
+    [webView setMainFrameURL:self.URL];
+  }
+  else {
+    jscocoa = [[JSCocoa alloc] initWithGlobalContext:[[webView mainFrame] globalContext]];
+    [jscocoa setObject:self withName:@"atomController"];
+
+    NSURL *resourceURL = [[NSBundle mainBundle] resourceURL];
+    NSURL *indexURL = [resourceURL URLByAppendingPathComponent:@"index.html"];
+    NSURLRequest *request = [NSURLRequest requestWithURL:indexURL];
+    [[webView mainFrame] loadRequest:request];    
+  }
+}
+
+- (void)close {
+  [(AtomApp *)NSApp removeController:self];
+  [super close];
+}
+
+- (BOOL)handleKeyEvent:(NSEvent *)event {
+  // ICKY: Using a global function defined in App.js to deal with key events
+  JSValueRef returnValue = [jscocoa callJSFunctionNamed:@"handleKeyEvent" withArguments:event, nil];
+  return [jscocoa toBool:returnValue];
+}
+
+// WebUIDelegate Protocol
+- (NSArray *)webView:(WebView *)sender contextMenuItemsForElement:(NSDictionary *)element defaultMenuItems:(NSArray *)defaultMenuItems {
+  return defaultMenuItems;
+}
+
+
+@end