engine: refactor code to replace stores in separate function
In not all upgrades, we need to change the whole store. For example, when upgrading repository to share-safe mode, we don't touch revlogs at all hence store cloning and copying is not required. The store replacing code needs to be made aware about what all has changed and hence only copy/rename those things. To kickstart that, this patch moves existing logic into a separate function. Differential Revision: https://phab.mercurial-scm.org/D9674
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