MDL-43848 messages: do not display message content in popups

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.
MDL-45485 auth_shibboleth: User taking over other user's session

Replacing code with call to complete_user_login() since it calls session_regenerate_id().
MDL-45616 repositories: more clearly distinguish when we use source and when reference

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
MDL-45616 repositories: use json encoding instead of serialization
MDL-45463 mod_lti: Prevent XML entity injections from provider
MDL-45417 mod_imscp: Prevent entity injections from package content
MDL-46148 qtype_calculated: fix formula validation.
MDL-45760 make sure to check permission before setting header
MDL-46223 Improve the rubric output
MDL-46223 Improve the marking guide output
MDL-43948 forms: setting types to filemanager and editor elements
MDL-45471 javascript: Escape content of exception dialogs
MDL-46223 Improve the display of marking guide validation message
MDL-46223 Fix frequently used comments in the marking guide

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