Steps to reproduce:

 * Running ikiwiki 3.20130904.1ubuntu1 on Ubuntu 14.04 LTS
 * Modify `~/public_html/MYWIKI/local.css`
 * Run `ikiwiki --setup MYWIKI.setup` (or update via websetup interface)

What should happen:

 * Setup is updated/site is rebuilt
 * local.css is retained and used

What happens instead:

 * Setup is updated (works)
 * local.css reverts to blank version

Workaround:

 * Create mylocal.css, and manually copy it over local.css every time