Just create a graft of the parent of your new root commit to no parent (or to an empty commit, e.g. the real root commit of your repository). E.g. echo "<NEW-ROOT-SHA1>" > .git/info/grafts
After creating the graft, it takes effect right away; you should be able to look at git log
and see that the unwanted old commits have gone away:
$ echo 4a46bc886318679d8b15e05aea40b83ff6c3bd47 > .git/info/grafts
$ git log --decorate | tail --lines=11
commit cb3da2d4d8c3378919844b29e815bfd5fdc0210c
Author: Your Name <[email protected]>
Date: Fri May 24 14:04:10 2013 +0200
Another message
commit 4a46bc886318679d8b15e05aea40b83ff6c3bd47 (grafted)
Author: Your Name <[email protected]>
Date: Thu May 23 22:27:48 2013 +0200
Some message
If all looks as intended, you can just do a simple git filter-branch -- --all
to make it permanent.
BEWARE: after doing the filter-branch step, all commit ids will have changed, so anybody using the old repo must never merge with anyone using the new repo.