I made the switch from Aptana 2 and am getting over the differences in the update. One change however, that I cannot get past right now is opening up one of my imported projects, which is Wordpress.
In my wordpress, I have it in its own directory, and moved the index.php and web.config file to the root of the project. I was able to edit while browsing the site from the root directory.
Now, in Aptana 3, when I jump to my localhost:8888 directory, which is ran by Microsoft WebMatrix, I get a Server error code 401.3. But when I close the project in Aptana and hit refresh in my browser, the page displays properly.
Further info, any sub-directories of the site run fine when I have the project open. Only root of the site is facing a problem. Never faced this while using Aptana 2.
Win7 x64, Aptana 3, IIS 7, WebMatrix
Try to unselect "Auto-detect modifications to projects made outside IDE" in Preferences/Aptana Studio and see if that helps.
FYI, "HTTP Error 401.3 - Unauthorized: Access is denied due to an ACL set on the requested resource."