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Initially I was looking at /template/en/custom/global/user-links.html.tmpl and curious why there is no upstream equivalent.

Our custom /template/en/custom/global/footer.html.tmpl is in use.
It defines the entire left toolbar (and the footer).
It processes the following custom files:
* /template/en/custom/global/user-links.html.tmpl
* /template/en/custom/global/nav-links.html.tmpl
* /template/en/custom/global/search-links.html.tmpl

In upstream code,
/template/en/default/global/footer.html.tmpl processes 
* /template/en/default/global/useful-links.html.tmpl 
which in turn processes
* * /template/en/default/global/common-links.html.tmpl

However, as upstream /template/en/default/global/footer.html.tmpl is the only file calling [% PROCESS "global/useful-links.html.tmpl" %], but as we have replaced upstream footer.html.tmpl by our custom /template/en/custom/global/footer.html.tmpl, this stuff is never called, so we won't see a "Saved Reports" item in the left pane in Bugzilla 4.4 once we have upgraded from 4.2 to 4.4, as <li id="reports-saved"> is defined in /template/en/default/global/useful-links.html.tmpl.

We should either port, or (preferably) adapt the upstream structure to minimize the diff here, get new functionality, and improve maintainability.