Thanks. Before I respond, understand that I’m coming back to Vim after an extended absence. Also that I am primarily a writer, not a coder. That said, I had a decent configuration for my uses and had gotten comfortable using it.
As to your questions: I don’t think there is any syncing. The two installations of Vim—MacVim and iVim—would never be used at the same time.
Likewise, the .vimrcs for the two installations are different: The one for iVim is simpler, to restrict operations to those permitted by the sandboxing of iOS apps, e.g., use of Vundle has been eliminated. The .vimrc for MacVim is installed in my root directory, the one for iVim in the documents folder of the iVim app.
The installation of Vimwiki is set up in the .vimrc of each installation and is identical in both cases.
Not certain I have adequately answered your questions.
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