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I have set

 templatedir => "/srv/apache2/madduck.net/templates",

in ikiwiki.setup and put a custom page.tmpl in there, then called ikiwiki --setup and verified that it works. It even works when I push to the Git repo and let the receive-hook update the wiki.

However, when I make a change via the CGI (which has been created by the last setup run), it applies the default page.tmpl file to all pages it updates.

Hmm, I tried to reproduce this, but failed, my modified template was used both during the --setup and for cgi edits.

Are you 100% sure that your ikiwiki.cgi is right? Try: strings ikiwiki.cgi |grep templatedir --[[Joey]]