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!