I don't think so. When updating the base system, all ports (apps) must be rebuilt, and the packages provided are built with just the default settings. You will get your default packages just fine, but you'll have to rebuild your custom app yourself.
That flaw is well known. When I update my system, I need to first deinstall my custom app, and build it again afterwards. There's no easy workaround, unfortunately.
Back in the days of 1997 I disabled each and every auto-anything setting right after installing that kind of software. It's annoying when I tell the software to do one thing and it does another.
Such as with many other conflicts, much of the mess is caused by lack of clarity of the meaning of things. A very well defined issue is broadened to handle a lot of unrelated things, and so it misses its substance. The Black Lives Matter movement is specific about unjustified violence by police officers against black people in the United States. As such, it is indisputable. When it turns out to involve slavery, ban racial terminology, offend white people, demolish historic monuments, be a left wing banner, it gets into the mess of useless political and racial debate.
My, oh my! Around here, people use to type KKK meaning "I'm laughing out loud!". Hardly anyone remembers KKK "up there". Slavery in computing systems. So what?! They are meant to be slaves. I want to keep a list of unwanted things. But the list cannot be black. I will be banned. Black is beautiful forbidden. When I say "black", I mean "a color", instead of "people with African origins". Why should anybody feel offended because of a color's name? (Just to keep you informed... it's winter here.)
How does NetBeans compare with Eclipse? Earlier I have heard that Eclipse should be good for Java developers.
Things have changed a bit. As I'm working with Maven, NetBeans is so much easier than Eclipse. But Intellij IDEA has catched up being the preferred IDE for many. I just prefer NetBeans because I'm used to it and it does what I need.
Markdown in which editor? Or is there an editor called Markdown?
Markdown is a formatting standard for plain text files. Any plain text editor can do it. Such a document can be viewed in plain text as is, or nicely rendered with structured formatting (such as styled HTML). Hence, a text editor with quick preview is preferred. As I am a Java developer, I'm using NetBeans IDE for Markdown editing. But it could be anything else. In Chrome-like browsers, there are extensions available which render Markdown files as nice formatted documents, and the browser itself is able to export them to PDF. That's OK for me. No Microsoft software in the way.
Was track changes already properly developed back then?
I think it was - although I seldom needed it, if at all back then. I can open DOCX pretty well with MS Word Viewer in Wine, with proper - official - filter formats added. If I needed to edit something with Word, I would use Word 97 (yes, it opens and edits DOCX), but I uninstalled it because of lack of use. For my editing needs, I use Markdown. If I have to publish something, I export it to PDF, and that's all. Let's say word processing is not one of my main activities nowadays.
When I needed MS Word, I installed Word 97 in FreeBSD on Wine. Works like a charm. Fully compatible with current Office formats. My wife used it to publish her post-graduation work.
In some areas, women aren't hired because they get pregnant. In others, they are hired because they are pretty. Strengths and weaknesses... But usually, people are hired because they can do the job.