- do not die with fatal error if source file in moodle internal repository is missing;
- moved code duplication for moodle repositories into class repository (functions send_file, get_reference_details, get_file_by_reference, get_file_reference);
- update file status after repository::sync_external_file so we know that it is missing (or not missing anymore). Do not run this function more than once for file within one request;
- display readable name for Private Files and Server files with the new format;
- display broken icon in filemanager if we know that source is missing, display information (for admin) where it was located before: see repository::get_reference_details() and extending classes;
- removed unnecessary queries in stored_file::sync_external_file();
- syncronize files before displaying it's size in mod_resource, do not query directly
- changed function repository::copy_to_area so it accepts more file attributes, pass changed attributes to it
- changed file_info::copy_to_storage and file_info_stored::copy_to_storage to accept more file attributes
- simplified file size check for moodle files in repository/repository_ajax.php
- removed unused code in repository/repository_ajax.php
- Removed 'Private files' from 'Server files' repository;
- Show only non-empty directories (taking into account filetype filter);
- If there is only one non-empty filearea within a module, do not show it and skip the extra subdirectory level;
- If the user is not admin (does not have 'moodle/course:update' capability in system context), do not show course categories, just list available courses;
- Also when retrieving the course files capability to managefiles is checked before retrieving the modules list for performance tuning on sites with a lot of courses
