Remove refs/original/heads/master from git repo after filter-branch --tree-filter?

I had the same question as asked here: https://stackoverflow.com/questions/7193507/new-git-repository-in-root-directory-to-subsume-an-exist-repository-in-a-sub-dire

I followed this answer here: https://stackoverflow.com/questions/7193507/new-git-repository-in-root-directory-to-subsume-an-exist-repository-in-a-sub-dire/7194124#7194124

Now, gitk --all shows two histories: one culminating in the current master, and one named original/refs/heads/master.

I don't know what this second history is, or how to remove it from the repo. I don't need two histories in my repository.

How do I get rid of it?

To reproduce yourself:

mkdir -p project-root/path/to/module
cd project-root/path/to/module
mkdir dir1 dir2 dir3 
for dir in * ; do touch $dir/source-file-$dir.py ; done
git init
git add .
git commit -m 'Initial commit'

Now we have the original poster's problem. Let's move the root of the git repo to project-root using the answer linked above:

git filter-branch --tree-filter 'mkdir -p path/to/module ; git mv dir1 dir2 dir3 path/to/module' HEAD
rm -rf path
cd ../../../ # Now PWD is project-root
mv path/to/module/.git .
git reset --hard

Now, see my current problem:

gitk --all &
git show-ref

How do I get rid of refs/original/heads/master and all associated history?

refs/original/* is there as a backup, in case you mess up your filter-branch. Believe me, it's a really good idea.

Once you've inspected the results, and you're very confident that you have what you want, you can remove the backed up ref:

git update-ref -d refs/original/refs/heads/master

or if you did this to many refs, and you want to wipe it all out:

git for-each-ref --format="%(refname)" refs/original/ | xargs -n 1 git update-ref -d

(That's taken directly from the filter-branch manpage.)

This doesn't apply to you, but to others who may find this: If you do a filter-branch which removes content taking up significant disk space, you might also want to run git reflog expire --expire=now --all and git gc --prune=now to expire your reflogs and delete the now-unused objects. (Warning: completely, totally irreversible. Be very sure before you do it.)

And if you're in Windows PowerShell:

git for-each-ref --format="%(refname)" refs/original/ | foreach-object -process { git update-ref -d $_ }

filter-branch keeps backups so repository need to clean up reflogs and garbage collect. Make sure that have no need in this backups before deletion:

rm -Rf .git/refs/original
git gc --aggressive --prune=now