I'm not sure if I understand the problem correctly. "root" for the plugin is

either the project directory itself, e.g. /home/techet/projects/geany
or added external directories, e.g. /home/techet/projects/geany-plugins and possibly some more

Since /home/techet/projects/geany is the directory containing the project, it doesn't make sense to ignore it - you wouldn't see any files in the sidebar if you did it. Similarly, it doesn't make sense to do this for external directories because you can simply remove those you don't want to see.

So how is your project organized - the mounted directories are mounted somewhere inside the project directory itself?

Couldn't the problem rather be in the "Index all project files" settings under Project->Properties->Project Organizer which, when enabled, parses all files (and possibly loads their full contents over network)?

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