Detach many subdirectories into a new, separate Git repository

This question is based on Detach subdirectory into separate Git repository

Instead of detaching a single subdirectory, I want to detach a couple. For example, my current directory tree looks like this:

/apps
  /AAA
  /BBB
  /CCC
/libs
  /XXX
  /YYY
  /ZZZ

And I would like this instead:

/apps
  /AAA
/libs
  /XXX

The --subdirectory-filter argument to git filter-branch won't work because it gets rid of everything except for the given directory the first time it's run. I thought using the --index-filter argument for all unwanted files would work (albeit tedious), but if I try running it more than once, I get the following message:

Cannot create a new backup.
A previous backup already exists in refs/original/
Force overwriting the backup with -f

Any ideas? TIA

Solution

Answering my own question here... after a lot of trial and error.

I managed to do this using a combination of git subtree and git-stitch-repo. These instructions are based on:

Sharing code between projects with git subtree – http://psionides.jogger.pl/2010/02/04/sharing-code-between-projects-with-git-subtree/
The Right Tool for the Job: git-stitch-repo – https://ifup.org/posts/the-right-tool-for-the-job-git-stitch-repo/

First, I pulled out the directories I wanted to keep into their own separate repository:

cd origRepo
git subtree split -P apps/AAA -b aaa
git subtree split -P libs/XXX -b xxx

cd ..
mkdir aaaRepo
cd aaaRepo
git init
git fetch ../origRepo aaa
git checkout -b master FETCH_HEAD

cd ..
mkdir xxxRepo
cd xxxRepo
git init
git fetch ../origRepo xxx
git checkout -b master FETCH_HEAD

I then created a new empty repository, and imported/stitched the last two into it:

cd ..
mkdir newRepo
cd newRepo
git init
git-stitch-repo ../aaaRepo:apps/AAA ../xxxRepo:libs/XXX | git fast-import

This creates two branches, master-A and master-B, each holding the content of one of the stitched repos. To combine them and clean up:

git checkout master-A
git pull . master-B
git checkout master
git branch -d master-A 
git branch -d master-B

Now I'm not quite sure how/when this happens, but after the first checkout and the pull, the code magically merges into the master branch (any insight on what's going on here is appreciated!)

Everything seems to have worked as expected, except that if I look through the newRepo commit history, there are duplicates when the changeset affected both apps/AAA and libs/XXX. If there is a way to remove duplicates, then it would be perfect.