manifest: Remove checkout to '.' which is not allow by repo
New repo version don't allow a checkout to '.'. The change was introduced to repo with: https://gerrit.googlesource.com/git-repo/+/a00c5f40e76fd520597013ae89823711212630b3
The config repo is now checked out to .conf directly and setup-environment is linked into the base folder.
BCS 746-000284
Change-Id: Ib293ec70458dad304baa9d8acb9b91f8898aee8a