I currently run Ubuntu Mate 16.04.6 on both my Thinkpad T430 and my homebuilt desktop machine (hardware continuously upgraded for fifteen years or so), and I'm interested in upgrading to Ubuntu Mate 18.04.2. I started the upgrader on the laptop, and was informed that tens of packages would be removed -- I presume because the upgrader only upgrades built-in packages and the packages in question were versions that weren't compatible with 18.04. The upgrader also disabled the repositories for "third party" packages, presumably for the same reason.
My question is, with a system that's not 100% "box stock" (which probably applies to nearly any install that's not used in a locked-down, IT-administered environment), will the "upgrade to 18.04.2" process be reliable enough to plan on simply updating the repo information for my other required packages (update-sun-java, BOINC, etc.) and reinstalling those, or can I look forward to "it'll take less time to install everything clean"?
In my experience, installing clean and reinstalling third party apps would have me looking forward to spending an entire weekend of free time on each machine, so if the upgrade is dependable, it would be preferred -- but spending two weekends, one upgrading and cleaning up after a broken upgrade, and the next installing the new version clean, with a week unable to use the machine in between, is obviously undesirable.