This catches things like:
 * Malicious equations coming from backup files.
 * Malicious equations in old questions in the database.

... when adding a dataset with a formula error.

In order to do this in a sane way, I cleaned up a lot of old mess,
inclduing:

1. Previously, qtype_calcuated used ->answeres when importing, and
->answer when saving the form. This was crazy, so I fixed it, and
stripped out the code that made the alternative variable name work.

2. Similarly, it could handle ->answer being either an array, such as
you would get form the HTML editor, or a simple string, which is what
you get form the form. I simplified that too.

3. Finally, I made import use a transaction around saving each
question, so we don't get half questions in the database when an error
occurs.

When the frequently used comment contains a character like >, re-use it
directly instead of its HTML entitiy.

Function repository::get_moodle_file() should always be called on packed reference and not on the source received from user.
Also added phpdocs to some other methods that were confusing source and reference

Replacing code with call to complete_user_login() since it calls session_regenerate_id().

The user is not in control of when these popups show up and it
may not be appropiate to have part of this content display whilst
in the presence of other users.