upps.. problem when rebasing (and subsequent nasties)

I'm still n00bing around with git, but I've got it into a state which has me confused..

In doing a git-rebase, I got a number of errors like

error: modules/realtime-app-ui/src/main/webapp/WEB-INF/faces-config.xml: does not match index ... Using index info to reconstruct a base tree...

What does this mean? I made matters significantly worse, but managed to save my bacon with git-fsck --lost-found, but now my working copy seems really unhappy. If I want to get back to my branch I try

git checkout thing

fatal: Entry 'modules/realtime-app-ui/src/main/webapp/WEB-INF/faces-config-core.xml' not uptodate. Cannot merge.

I just want to get back to the start, so I git reset --hard git checkout foo fatal: Entry 'modules/realtime-app-ui/src/main/webapp/WEB-INF/faces-config-core.xml' not uptodate. Cannot merge.

I can probably recover it by blatting everything and starting over, but I'd like to know what the mess is that I've managed to get into so I can avoid it in the future!