Regenerating default overlay in gentoo

Question

Could not sync portage for some time - realizing it was because I was using git as sync method and the repo was not maintained anymore. They also provided new links so I updated sync-uri option in /etc/portage/repos.conf/gentoo.conf

[gentoo]
location = /var/db/repos/gentoo
sync-type = git
#sync-uri = https://github.com/gentoo/gentoo-portage-rsync-mirror  # old
sync-uri = https://github.com/gentoo-mirror/gentoo                 # new
auto-sync = true

But this was without effect when running emerge --sync:

# emerge --sync
>>> Syncing repository 'gentoo' into '/var/db/repos/gentoo'...
/usr/bin/git pull
Already up-to-date.
=== Sync completed for gentoo

Today I realized that I can check remote url of the repository:

# cd /var/db/repos/gentoo
# git remote -v
origin  https://github.com/gentoo/gentoo-portage-rsync-mirror (fetch)
origin  https://github.com/gentoo/gentoo-portage-rsync-mirror (push)

So it is still set to the old one.

I tried to change it to the new one, but it was first complaining about git config and even after that I could not sync:

# git remote set-url origin https://github.com/gentoo-mirror/gentoo
# git remote -v
origin  https://github.com/gentoo-mirror/gentoo (fetch)
origin  https://github.com/gentoo-mirror/gentoo (push)
# git config user.email "root@gentoo.xxx"
# git config user.name "Root One"

# emerge --sync
>>> Syncing repository 'gentoo' into '/var/db/repos/gentoo'...
/usr/bin/git clone --depth 1 https://github.com/gentoo-mirror/gentoo .
fatal: destination path '.' already exists and is not an empty directory.
!!! git clone error in /var/db/repos/gentoo
!!! Repository 'x-gentoo' is missing masters attribute in '/var/db/repos/gentoo/metadata/layout.conf'
!!! Set 'masters = gentoo' in this file for future compatibility

So at the end I ended up with deleting whole directory /var/db/repos/gentoo except distfiles/ with ls -a | grep -v distfiles | xargs rm -r which solved my problem and I could finally sync..

Question is: is there some user friendly / right way how to recreate/regenerate gentoo overlay which is using git?

I think more people will have this problem once repository of overlay will be changed.