See the good news - how Ubuntu-Mate fixed the broken bootloader for me:
A further warning - there seems to be problems with the version of JAVA included in the 18.04 base. If you run JAVA-dependant programs beware...
Edit (04.09.2018)
This is a link to the post I made explaining how I was able to get my Java-based programs running again:
This did not fix all my problems though, pdfsam will still not launch. As pdfchain has also been caught out by the new technological base of Ubuntu 18.04, I currently use Master PDF Editor for pdf manipulation.
Despite all the good work done by Canonical and the Ubuntu-Mate team, if you use Ubuntu-Mate 16.04 in a "production" environment i.e. you use it to earn your income (or a part of it) I would currently advise caution, and waiting to upgrade as long as you can, preferably setting up a test system 18.04 to make sure you know what will happen to your regular tools.
