Don't grey out Sky code in Atom

For some reason having |packages| in this .gitignore file is causing Atom to
grey out all the files in the Sky package. Moving the entry up to the root of
the git repo fixes the issue.

packages/flutter/.gitignore

@@ -2,5 +2,4 @@
 .pub/
 AUTHORS
 LICENSE
-packages
 pubspec.lock