As developer Anders Borum told me, one of the nice aspects of this integration between Working Copy and external folders is that all the Git housekeeping data (usually stored inside a .git folder) will be kept inside the original app if it’s already there; if it isn’t, however, Working Copy will keep the .git directory for itself, so it doesn’t “confuse” the linked app. Essentially: if you connect an app like Obsidian to Working Copy as a linked repo, don’t worry about any .git data being copied into your Obsidian vault.