Perhaps AGN ZC will be more about emulating Zelda 1 and ZQuest Classic will be more about being a fully-featured game engine that happens to run quest files made for ZC 2.55 and below?
By the way, git history doesn't necessarily take up gigabytes of space as the git system compresses the differences. I personally have in the past migrated a self-hosted SVN to GitHub, at first using a hook to sync the two before retiring the SVN in favor of Git. All history was maintained, except for some extremely early revisions that were lost when my first VPS provider suddently went under.
Git repos are designed to be cloned as I said multiple times. The ZQuestClassic repo can be cloned using any Git tools you want.
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