make manifest usable in worktrees

Context

When running the manifest tool, it is checking that it is at the root of the project by looking for a directory named .git, however, when you use git's worktrees, the root directory contains a .git regular file that contains the actual path of the main git repo.

Manually testing the MR

create a git worktree and try to update the manifest. Before the modification it fails, after it works.