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I'd stop using things like App Cleaner, again you don't need to uninstall stuff on macOS before installing a new version, and if anything ever went wrong with stuff you should know what you are doing. macOS is not Windows, it normally does not need to be abused to work. Stuff like this or running antivirus software of macs is likely to just cause more problems than it solves.
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Good advice.
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Maybe other folks have suggestions, I do recall one weird case that this reminds me of but my recollection is really bad about it and I could not find the thread.
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This mess started the second my MacPro hit the Avid server after my reinstatement. Technically I don't know what changed, but as dumb as it sounds it's when everything went south.
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You can try looking in the Pro Tools logs ~/Library/Logs/Avid/Pro_Tools_* Logs can help occasionally and you may be at a point so early in the startup that they are empty or don't even get created. But sometimes stuff stands out there, especially if you can compare to old logs from successful runs. Sometimes you might also see an odd warning or error message in syslog (in Console.app).
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I compared a normal PT bootup from 7 days ago to a new one and there was a whole lot of extra crazy stuff going on near the beginning of the process.
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Anyhow it seems you are at the point of probably don't waste more time on troubleshooting and either restore from backup or grab a spare new clean drive or create a volume/container on a existing drive and do a install of macOS and Pro Tools on that and just test it works at all, if so install other plugins and apps and switch over to using that volume as the boot volume. Only reason to suggest caution here is an assumption you have other apps or documents on the existing boot drive and best not to blow that away until you know everything works OK and you can the do a careful manual move of files between the old and new boot volume (or use macOS migration assistant to move *accounts* but do not use it to move drivers or apps).
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I make system drive clones whenever I upgrade OS, I just booted up with May's 10.12.6 clone (with old installs) and everything works now. It sux that I had to spend $499 just to lose 4 days of work and my sanity. Again, many thanks for your input.