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git.directory: Initialize git submodules after switch to git ref

Antoine R. Dumont requested to merge directory-fix-submodule into master

Without this, some git clones are failing to be ingested because they referenced submodule which is not initialized. This results in hash mismatch since the git tree checkouted does not match the upstream nix/guix manifest.

This solves partially [1]

[1] Refs. #4751

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