simon, hi, many apologies for not following up: my friend running the server discovered, after around 18 months of puzzled investigation, that he had (or perhaps had not) added a certain critical system-required file to .gitignore as part of the upgrade to gitolite3. exact details are hard to remember (plus it wasn't me doing the investigating) but this was very obscure, but finally solved.
the typical ikiwiki git arrangement was as you described. although it would only be a kludge, the "manual recovery" i propose(d) would be an "rm -fr * and a git clone", or a "git reset --hard". this would at least permit people in similar circumstances to at least run a functioning web site from a remote laptop whilst there was a sysadmin (2nd person) who could only respond on a delayed schedule. l.
