How can I rewrite history so that all files, except the ones I already moved, are in a subdirectory?

To rewrite the history with the files moved:

If you want the project's history to look as though all files have always been in the directory foo/bar, then you need to do a little surgery. Use git filter-branch with the "tree filter" to rewrite the commits so that anywhere foo/bar doesn't exist, it is created and all files are moved to it:

git filter-branch --prune-empty --tree-filter 'if [ ! -e foo/bar ]; then    mkdir -p foo/bar    git ls-tree --name-only $GIT_COMMIT | xargs -I files mv files foo/barfi'

Now the history will be recorded as if all files were always located in foo/bar.

To see the history of a moved file:

If you just want to see the history of a file that has been moved or renamed at some point in the past, then simply use the --follow option to git log:

git log --follow foo/bar/file.c

To wrap things up here's a short summary of what I did. The command that worked for me was:

if [ ! -e foo/bar ]; then mkdir -p foo/bar; git ls-tree --name-only $GIT_COMMIT | grep -v ^foo$ | xargs -I files mv files foo/bar || echo ""; fi

The echo command that I added at the end ensured that even when mv fails entire command will continue running. It didn't move contents of foo/bar/foo, but I can live with that.

Thanks a lot to Dan Moulding (!!!) and Jefromi for the help.

Install git-filter-repo:

git clone https://github.com/newren/git-filter-repo/

Add the git-filter-repo executable to your $PATH (see INSTALL.MD for other options):

# this is just an example, you probably want to edit bashrc,# or add a symlink to ~/bin or /usr/local/binPATH=$PATH:${PWD}/git-filter-repo

Now cd to the git repo that you want to modify, and run:

git filter-repo --to-subdirectory-filter foo/bar