Only update Git submodules in cache when necessary

This saves a duplicate `git remote update origin` that was being run as
part of each chunk build. For any repos that have submodules, it also
avoids updating repos if the SHA1 we need to build is already present
locally.

As well as speeding up builds slightly, this means Morph can now build
without being connected to a network, as long as the local Git cache
all of the necessary repos and commits in the build, without needing the
'--no-git-update' option.

The code is also now in a more logical place than before.

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