Switch the compiler over to using ~[] notation instead of []/~

This is part of Issue #2653.

The compiler needs to be moved to using our new vector notation. Graydon produced a perl script to do the modification (https://gist.github.com/44083e642fc8422d60a3). The script chokes on unbalanced brackets, so I am working around that by adding closing brackets to unmatched brackets in comments. Some cleanup is also needed after running the script.
