Revert "project: initialize new manifests in temp dirs"

This reverts commit 07d21e6b.

Reason for revert: crbug.com/gerrit/16230, b/244467766 - breaks aosp-master-with-phones case

Change-Id: Id967d92f8622c2c13356b09e46ece9f20040aabc
Reviewed-on: https://gerrit-review.googlesource.com/c/git-repo/+/344314


Tested-by: LaMont Jones <lamontjones@google.com>
Reviewed-by: Xin Li <delphij@google.com>