That’s a new one to me. The error does look somewhat benign though.
There is an option to openhab-cli that can do that. See Clear the Cache. It’s a little important to make sure to stop openHAB before clearing the cache.
@Benjy, is this an oversight in the apt package? Should I file an issue? It seems like it should warn before overwriting /etc/default/openhab2 just like it does the other config files. Maybe there is a reason it doesn’t?
No is the time for me to make my Ansible pitch. I no longer install nor configure anything by hand any longer. I do it all through Ansible. Why? Because once it works I have my system configuration captured in code and rebuilding or repairing a system is a simple matter of running my scripts again. I frequently need to go back to them to remember where I put things or how I’ve configured things and the like. The short amount of time I spent up front to learn it have been more than recovered.
In fact, I don’t take full machine backups anymore. I backup the data and if I ever need to recover from a disaster I can just start from scratch and run the Ansible playbooks and I’ll be back up and running, usually in minutes.
Over the past few months there have been a huge amount of changes to JSR223 and the helper libraries. The docs have not been kept up. We are waiting for a number of significant changes to be merged before we recreate the docs. But I was unaware that the OH Docs right now still uses /etc/openhab2/lib and not /etc/openhab2/automation/lib. automation has been the right place to put them for quite some time.
This is a good candidate for a first PR. 
Click the link at the bottom of the page and it will take you to the file in github where you can make the changes in the browser. You will need a github account. See How to file an Issue for details.
At a higher level, to address your recommendations, any recommendations made here on the forum are unlikely to be acted upon. They need to be filed as an issue on github.
Chris has been hard at work improving Zwave for sure.
Lack of MQTT support in a hub in this day and age is a huge oversight. MQTT has become the lingua franka of IoT. At least among those of us who are cheap and possess just a little bit of skills.