This was fixed.

wiki.bugzilla wrote:

Reopened: see http://www.mediawiki.org/wiki/Image:Monobook-cologneblue-standard.png

Added "simple skin" to the summary because it's also affected slightly.

Using one of the 3 skins CologneBlue, Classic/Standard or Simple, only
the first section of the main navigation/sidebar is displayed and/or many
items are missing, especially if there are subdivisions in [[MediaWiki:Sidebar]].
The amount of missing links is due to the particular content of MediaWiki:Sidebar
and its specific sorting on each project.
But newly created links are also missing sometimes if there are no subdivisions.
I didn't manage it yet, to figure out the actual scheme behind the incomplete
display for more than a few projects/languages.

For example with Simple on MediaWiki.org only one link of the resources
section is missing, on Commons the whole third section isn't displayed.

Also the existence of an incompletely translated MediaWiki namespace (in
case of every new sidebar related message pair foo-url|foo) seems to affect this.
In case of such a missing translation at least the default link (english) should
be displayed, not only an empty space in the sidebar (observed with "Simple").

Presumably there are several more links in the GUI of all non-Monobook skins,
that aren't displayed at the moment but ought to be, of course.

So a general rework of the skins is badly needed (perhaps consider removing
some silly skins for Wikimedia projects; we already got MySkin for gadget).

This is a request for ongoing maintenance. Please make sure, that the full set of
links is available in the GUI of each skin.

ahz wrote:

Into skins the cologneblue and classic is sidebar not
complete navigation on the left of that and it are
missing on the left of to important sides.

Looks intentional. We explicitly only use the first toolbox
in the cologneblue skin.

That doesn't sound particularly intentional; there didn't used to be support for
more than one afaik.

Created attachment 5699
Update for cologneblue and standard skins to support more boxes

The attached patch fixes the issue while retaining basic skin characteristics:

• Standard skin has no section headers displayed
• Standard skin adds contributions and watchlist at the end of the "browse" sidebar
• CologneBlue skin has its own message "qbbrowse" that overrides the "browse" sidebar
• Nostalgia has still no boxes at all

Attached:

Fixed in r83863