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turns out this value does not take effect until there is a restart. I can not find a command to restart blender, so while this value does change successfully, it no effect on testing.
It's not needed to set the script directory in the preferences while running blender. It's possible to set the environment variable BLENDER_USER_SCRIPTS before starting blender. I do this in the script, that's firing up blender-addon-tester and it works fine, although it would be nice, if blender-addon-tester would take care of this.
I think i have figured out what was wrong, when you are installing you need to define the target, if you don't it just uses the default, use target='PREFS':
A feature was added to change the location of the addon installation.
bpy.context.user_preferences.filepaths.script_directory = addon_dir
turns out this value does not take effect until there is a restart. I can not find a command to restart blender, so while this value does change successfully, it no effect on testing.
https://docs.blender.org/api/current/bpy.types.PreferencesFilePaths.html#bpy.types.PreferencesFilePaths.script_directory
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