change paths in manifest/einsteintoolkit.th to be able to use GetComponents to restore missing symbolic links

This patch changes the CHECKOUT path description of the git repos that are checked out whole into directories (manifest, utils, CoreDoc among them).

Most likely due to way GetComponents decides if a component is already checked out, the previous version would not succeed in actually restoring a missing "manifest" symbolic link when it was deleted manually and GetComponents used to restore it. Ie.

GetComponents https://bitbucket.org/einsteintoolkit/manifest/raw/master/einsteintoolkit.th cd Cactus rm manifest bin/GetComponents repos/manifest/einsteintoolkit.th

will not restore manifest.

Pull request is here: https://bitbucket.org/einsteintoolkit/manifest/pull-request/3/einsteintoolkitth-change-checkout-so-that/diff

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