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This sounds very similar to the issues I'm experiencing. +1 to this.

Upon further inspection, the problem might be unrelated to git. Object variables simply won't be applied to instances. Neither will the assigned flow or state macros.

A cool way of bringing it one step further would be to include the graph data in the PNG itself, so that you can import the graph directly into Bolt by dragging and dropping a PNG. PICO does this and it's just magical.