you need to reach its developers and/or maintainers and ask them to start doing this via jmeter-plugins support forum
More information:
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Pau,
In the PR, I did exactly what you asked for: use plugins manager
JAR location for determining the place to write the libs.
I'm not familiar with Flatpak and have not much spare time to work on this. As suggested above, probably you can manipulate some search paths for JMeter to have a specific writeable place where plugins manager would reside, together with plugins.
The way JMeter works requres plugins manager to be placed into searchable location, I cannot change that.
You have the source code of the branch, you can experiment with it and do your custom builds of plugins manager.
Good luck!
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Andrey
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