I have two hard disks: One with the operation system Debian 11. On this hard disk I saved the Cryptomator Appimage. On a second hard disk I saved my personal files as the safes of Cryptomator. The second hard disk is mounted on /media/festplatte device /dev/sdb1. Starting the Appimage Cryptomator finds pathes and safes. But starting the Flatpak Cryptomator doesn’t. I even can’t change pathes because Cryptomator doesn’t find them.
Hello @nullproblemo
I found your post in a search because I am having exactly the same problem on Manjaro. Previously used the AppImage, everything was fine but the Flatpak wouldn’t find my vaults.
It is, I think, a problem with the Flatpak build permissions. The build doesn’t have access to your mount point, but there is a way to add it - but I came on here because I found that the change would automatically get reversed and I’d have to run the command again.
You can give the Cryptomator Flatpak complete access to your host file system, with the following command:
sudo flatpak override org.cryptomator.Cryptomator --filesystem=host
I preferred not to and manually stated where on the file system I wanted the Cryptomator Flatpak to have access to a specific moutn point, so yours would be:
sudo flatpak override org.cryptomator.Cryptomator --filesystem=/media/festplatte
You can provide multiple filesystem options, so you could do any number of mount points, for example:
sudo flatpak override org.cryptomator.Cryptomator --filesystem=/media/festplatte --filesystem=home
The above would give you access to the festplatte mount point and your home directory (including all subdirectories).
Hopefully one of the dev team might spot this and be able to comment/fix a later Flatpak build - I was searching for a thread to ask the dev team if they could fix it in a later build 
I love Cryptomator, recently purchased my supporter certificate. Brilliant piece of software. Hope this reply helps you 
EDIT: Should have said, best to run the commands without the Flatpak running - if it’s running you will need to restart Cryptomator for the changes to take effect.
Hey and welcome to the Cryptomator Community 
,
Thank you both for the feedback and I can confirm, because of we set --filesystem=home in org.cryptomator.Cryptomator.yaml#L12, the Flatpak version of Cryptomator can not open vaults from everywhere on the system.
We will discuss what we can do here but thank you for sharing your thoughts and @Encrypt-This for the provided workarounds.
Thank you both for your answers!
Thanks, I could now open my vaults in external usb folders. Something happen, I can’t close cryptomator after that…
Sorry I am using french language…
You can adjust the Flatpak permissions using Flatseal
That way you can give Cryptomator access to some other paths than home. Works for me, I have the same setup.
Yes, this works fine. Nice idea!
some other path ?
What other path are you suggesting ?
I’m not sure i’m finding it secure enought to let it access to filesystem=host
isn’t there a way to tell it to always open it to /mnt/cryptomator/[vaultname]
appimage format are fun, but need a bit more work to add them to the menu
This only applies if you are using the flatpak version of Cryptomator.
It’s not a massive inconvenience as a workaround, but good to know you are aware 