I must be doing something wrong. Running setup:

$ ikiwiki --setup MyIkiwiki.setup

overwrites my local.css with the default (empty) version.

I am using ikiwiki_3.1415926.tar.gz installed into /usr/local.

Sorry. Never mind. RTFM. --refresh duh.

Hmm, well. Using --refresh is a good thing because it allow ikiwiki to update a site quicker. But, it must only be hiding the real problem. Sounds like you are trying to edit local.css directly inside the destdir. But ikiwiki has a local.css located in its basewiki, so when you rebuild your local mods are lost. Fix is to put you locally modified local.css inside the srcdir, along with the other pages of your wiki. --Joey