5.) If you add a hyperlink in a note it is broken with makesafe() turned on.
I'm not sure this has anything to do with makeSafe(). Right now makeSafe() is effectively disabled and I've carefully reviewed the changes to addAppNode.php but I can't see how any of the changes broke notes.
On my local machine after previewing a note I'm seeing any url I put in prefixed by the current page url. On the appdb when previewing everything appears to be working correctly.
I think this may be a legit bug with the injection changes and I'll fix it before committing.
Just tested again here with the injection changes and hypertext(tested with a url) in notes looks good to me.
Chris