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I use Inno Script Studio to generate the actual installer. There is nothing I can actually think of that caught me out, other than it just took some time to figure everything out (like admin rights, banner graphics, unlocking directories etc).

I recently had a lot of problems with using the App Builder to create an installer. In the end I gave up and used Inno Setup and was pleasantly surprised.

Well, one big advice: Try to avoid merging as much as possible. Unlike with text sources where there is often automatic merging possible and you only have to glance over it to make sure nothing stupid has been done, graphical merging is still a fully manual job. The merging tool shows you the differences and lets you decide which changes should be copied into the master but it will not do any automatic merging. That alone is a big incentive to only really merge if there is absolutely no other way around it. We have found that it is easier to ensure that no two people are ever working on the same VI to avoid the merging hassles afterwards. Graphical merging is still in its infancy and I'm not even sure there is an easy way to reach the same level of automatic merging than with text sources. Text is fairly one dimensional in structure, while graphics are at least two dimensional and in the case of LabVIEW in fact more like 2 1/2 dimensional. Automatic text merging can still suck too, if two developers happen to make changes to the same text lines, but for LabVIEW merging the smallest unit of measure for automatic merging is still a VI.