How do I prevent arduino acting like a virus all over my system?

I like arduino and I want to use it but the IDE is a disaster.

1 - I don't want it to use a directory 'Arduino' in my home directory, if everything I installed did that I'd have dozens (if not hundreds) of directories in my home directory. It should be possible to install it in a system directory or maybe in /opt.

2 - It should use the normal system configuration areas, not a unique directory called .arduino or .arduino15

3 - It shoudn't put a load of libraries and other files in the .arduino15 configuration area

Yes, I changed the sketchbook.path in preferences.txt in ~/.arduino15 and that prevents the creation of ~/Arduino but that's when I noticed all the files under ~/arduino15/packages. Most of these seem to be in the base arduino installation as well. What a mess!

I'm not surprised that newer versions of the Arduino IDE haven't got into the major distributions, they really aren't to well organised!

Is there any information anywhere about how one can do a 'tidy' installation?

It is much less intrusive than many other pieces of software.

As there are many, many, many, thousands of users It would seem it is not as bad as some might think at least.

Not knowing what OS you are running leaves some things to pure guesswork ?

There is of course the PORTABLE installation which may suit you better but even that will need some structure to dependencies of folders and locations.

You can google ARDUINO PORTABLE as there are lots of hits for that.

It's easy to use the Arduino IDE in portable mode. That will allow you to have all files related to the Arduino IDE under one folder if you like. You can put that folder anywhere you like on your system. It doesn't require you to do anything special except to create a folder named "portable" under the IDE installation folder:
https://www.arduino.cc/en/Guide/PortableIDE

chrisisbd:
I noticed all the files under ~/arduino15/packages. Most of these seem to be in the base arduino installation as well. What a mess!

The Arduino IDE comes with a version of the Arduino AVR Boards hardware package installed. When you update to a new version of Arduino AVR Boards, or install any other hardware package via Boards Manager they're installed to ~/arduino15/packages.