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.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