Linux flatpak install. Can't choose all dirs

I just installed KiCad via flatpak. When I start a new project I can’t choose from all folders on my system (not listed).
I usually store stuff inside a fold at the root dir. “/data” which is owned by root but has read, write and execute rights for everyone. Nevertheless it is not listed in the choose-able folders for saving projects. Why is that?

Because flatpak by default restricts access to a lot of things, including file system, except for some predetermined paths.
Use flatseal or cli commands to give access to kicad to paths you want.

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Extremely bad idea, this kind of stuff should be stored in your $HOME directory tree.
The / filesystem will be flattened when you do a system update.

So how do you work with several people on the same project? The unix way is to use folders owned by user:group are for.

I don’t know which kind of distro you use, but mine doesn’t do that…

Explanation I installed just KiCad with flatpak on my Debian, since that still ships version5

First, I stay away from snaps and flatpacks.
But anyway, it sounds like you have a setup with a “master file machine” with all the files, and you let other users access those from their own machines, is that right?
I only run a single-user machine with / on its own partition and /home on a second. This leaves me free to do full upgrades on the system and even reinstall without fearing my data could be lost.
If your /data is on an own partition, you may be able to do that as well.

One way is to is to create a directory under /home/groupname that is owned by the coordinator but has group permissions to members of the group. Nothing says that there must be a corresponding groupname in the users (password file).

In general user files should stay under /home. Top level directories should be left to the system.

+1
Additionally, managing user/group permissions are much easier at this level and incurs no danger of unwanted access to /

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