MDL-42815 Backup/restore: Error saving files - log messages unhelpful

This commit contains three changes in the three files:
1. A bug in the backup process meant that anything logged after a
   certain point did not appear in the on-screen display of the
   backup log, because the logger was serialised and deserialised
   but display code referred to the old version. Changed so that
   code retrieves new object.
2. Add more information to backup log when there is a missing file.
3. Add more information to restore log when there is a missing file
   (and remove existing code duplication of the current message).

The 'missing file' situation is one that generally shouldn't occur in
normal usage, but when it does happen, it is useful to have full
information about the file.
MDL-43071 assign: Fix offline grades import for scale grading.
MDL-42487: Forced userprofile dl style to be displayed: inline-block.
MDL-43150 tinymce_managefiles: fixed unattractive background
MDL-43164 JavaScript: Use the up/down move icon for non-AJAX courses

When a course format does not support AJAX, or AJAX is disabled at the site
level, we should revert back to the old-style move icon.

This helps to clarify that you cannot drag/drop the icon, but must click
instead.
MDL-43087 testing: ability to load features from additional paths
MDL-43092 theme_afterburner: Activity or Resource dialog greyed-out for non-empty courses
MDL-43192 Repository: param doesn't exist - should use function
MDL-43194 JavaScript: Correct maxlen jshint configuration
MDL-40213 theme_clean: Layout "secure.php" missing settings.
MDL-43202 JavaScript: Migrate moodle-course-toolboxes to user Shifter
MDL-38775 JavaScript: Migrate moodle-form-shortforms to Shifter
MDL-38776 JavaScript: Migrate moodle-form-showadvanced to Shifter
MDL-43212 JavaScript: Remove deprecated moodle-enrol-notification
MDL-40517 deprecatedlib: remove functions

* Removed functions which were throwing fatal errors
* Fixup navmenu comment, as it hasn't been throwing a fatal error, it
  shouldn't be removed as part of this issue yet. (Although if you are
  still using this function, you are crazy and should thank me ;-)).
MDL-37517 testing: remove deprecated classes
MDL-43215 core_webservice: retrieve all user name fields when adding a token
MDL-42174 More behat tests for filepicker
MDL-42174 behat: deprecate upload file to filepicker step in favour of filemanager
MDL-42174 behat: change word filepicker to filemanager in step definitions