refactoring a branch with e.g. meld how?

I've been asked to seriously reorganize and compress a big branch (75 commits)

What I'd like to do is make branches foo_flattened with all commits
and branch foo_reorganized
starting at the ancestor, then work by incrementally doing
meld/commit/meld/commit/etc from foo_flattened into foo_reorganized.

I hoped to use git difftool -d foo_flattened foo_reorganized, taking
advantage of the symlink behavior on the right hand side, but it links
the individual files not the entire working tree, which isn't too
useful since a lot of the changes introduce files.

Is there a git command to help with this or should I just be making a
copy of the entire foo_flattened tree and work from that?

I recall running across some command that I think was supposed to let
you have coexisting working trees of multiple commits or something,
but I can't find it now.

Britton