First a few goodies/responses…
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You’re right about not everything being exposed via the API. For what is exposed this may help: Sketch Lines - Edit, Copy, Paste - #20 by jacob.small. I do thing that there should be some out of the box nodes added for this.
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Grouping inputs is the generally accepted convention for the first part. You can also use the TuneUp view extension to ‘go to’ a given node. External input order will certainly help, but isn’t tracked anywhere I know just yet.
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The order is under review already. Hopefully we’ll have some good news in the near future.
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This is a bit harder as it would require opening all graphs to ID the lack of input. With Dynamo that is not a trivial task as you know; even with a text editor that could be cumbersome. Would the delay in opening a new folder be worth it?
Not all great news/insight, but hopefully some things put a bit of a smile on your face.
For the rest, the Dynamo development team has a public facing wishlist, here: GitHub - DynamoDS/DynamoWishlist: This is a repository for all wishlist items for Dynamo Core.
Any time you have an idea on something which could make an aspect of Dynamo better you can post a new ‘issue’ there. The team reviews these periodically and slots stuff into the relevant work-plans as applicable/possible.