When you use layers every piece will have the exact same axis. Just place the layers on top of each other with mask=1.
There should be some option where I can manually determine how many tiles I want at X and Y (that way I can avoid slacing something that doesn't need to be indexed couple times).I don't fully understand what you're asking, could you rephrase this maybe?
Some % progress bar somewhere would be real good too. Maybe at the system bar.Sure.
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