MDL-44844 core: Fix custom menu navigation

Atto introduced a rule to hide all Nodes with the yui3-menu-hidden class
but this rule is too general and applies to non-atto content too.

As a result, when loading the menu and during the XY calculation, the
native Element.getBoundingClientRect() function was returning a bounding
box size of 0 because the Node was not visible and the node was being
hidden from view when it was later made visible.
MDL-44936 csslib: Chunking supports @media queries and commas in rules
MDL-45048 repository_wikimedia: Abusing usage of optional_param

The optional_param call was moved outside of the constructor
because it was called every time the repository would be initialised.
That was leading to problems when the parameter was defined from
another form and not complying with its expected type.
MDL-44366 rework glossary filter caching
MDL-44366 bump up glossary and filter version
MDL-44366 improve glossary filter performance

This should have when there are no glossaries in course or
when there are no linked entries in existing glossaries.
MDL-44910 enable new logging during upgrade and installation

The legacy logging is now enabled for reading only
if legacy log data older than one day exists.
MDL-45009 Tex filter: Add \( \) delimiters for 1:1 compatibility with MathJax
Merge branch 'MDL-45048-master' of git://github.com/FMCorz/moodle
Merge branch 'w16_MDL-44910_m27_logupgrade' of https://github.com/skodak/moodle
Merge branch 'MDL-44844-master' of git://github.com/andrewnicols/moodle
Merge branch 'w16_MDL-44366_m27_filtergloss' of https://github.com/skodak/moodle
Merge branch 'MDL-44936-master' of git://github.com/FMCorz/moodle
Merge branch 'MDL-45009-master' of git://github.com/damyon/moodle
MDL-45047 Put the deprecation warning into mod/upgrade.txt, too

It is already in the main lib/upgrade.txt but it should be mentioned here as
well.