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manifest: Remove checkout to '.' which is not allow by repo

Tobias Kahlki requested to merge fix-repo-incompatibility-of-manifest into dunfell

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

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