Those downloads do indeed work "out of the box" with no additional configuration. If you notice otherwise, please do let us know.
What you cannot necessarily do, though, is install old extensions such as BoneJ1 and expect them to work with the latest version. While we have historically tried very, very hard to maintain backwards compatibility forever across the entire ecosystem of existing ImageJ plugins, in the case of Java 3D + Java 8 it simply became impossible to do so.
The term "Life-Line" was chosen by the previous maintainer of Fiji, who is also not a native English speaker. If you have a suggestion for terminology that would communicate the ideas more clearly—that these are old, stable versions of Fiji for use when the latest has some issue with your workflows—please feel welcome to edit the wiki to describe things in a better way. It would be most appreciated!
I am very glad to hear that these programs are useful to you!
I am sorry the current situation is a source of stress for you. Please feel free to use this forum to get your questions and concerns answered quickly. We very much want to help you minimize that stress!
If you describe what you want to accomplish, we can point you toward the simplest way of achieving it.
When you see outdated documentation—especially a page that you wish was current—please complain loudly. Then someone might have time to update it. Or at least give tips on how you could go about doing so.
The top-level source for ImageJ is at: https://github.com/imagej/imagej
The top-level source for Fiji is at: https://github.com/fiji/fiji
When you build, these projects will link in all the plugins as precompiled JAR dependencies. In NetBeans, it should be as simple as importing the source from the Git repository. You can use any Maven-based project you want with that approach, not just ImageJ. So e.g. you can import fiji/fiji that way, or an individual plugin such as fiji/AnalyzeSkeleton.
Start from imagej/minimal-ij1-plugin, edit the
pom.xml to your liking, and then import into NetBeans. Then edit the sources as normal, and you are good to go.
You can also write scripts and plugins in the Script Editor, which is intended to be a beginner-friendly development approach (as compared to IDEs, which many scientists have complained are too complicated for their needs).
Again, we are here to help, should you have the time and energy to invest.