Just a note to anybody using Cryptomator with Linux. At least with 16.04 LTS, gvfs is a bit unstable. So the nice way Cryptomator mounts your vault via DAV and gvfs means a few things:
Sometimes the application accessing the gvfs volume (/run/user/1002/gvfs/blah) will hang hard. No ctrl-C or Ctrl-\ will save you. The workaround is to kill -9 the application (or xkill it) lock and re-unlock the vault.
Since there are a variety of File dialogs on Linux, some applications will not be able to see the nice gvfs mount.
Unfortunately I have to confirm this (using 64-bit Linux Mint 18.2 MATE, which is based on Ubuntu 16.04 LTS) and looks like this prevents me of using Cryptomator at all as I am using Linux as my main system. In my case I tried to use VLC with Cryptomator and result was fatal - only reboot helped… Tried even newer kernel 4.12.11-041211-generic (64-bit) and this did not help either. This is unacceptable that in the middle of working just everything hangs and in my case I could not get no access until rebooted the computer. Cryptomator just said that one instance is running and it will exit:
[main] INFO org.cryptomator.launcher.Cryptomator - Starting Cryptomator 1.3.1 on Linux 4.12.11-041211-generic (amd64)
[main] WARN org.cryptomator.launcher.InterProcessCommunicator - System property cryptomator.ipcPortPath not set.
[main] DEBUG org.cryptomator.launcher.InterProcessCommunicator - Connecting to running process on TCP port 43667...
[main] INFO org.cryptomator.launcher.Cryptomator - Found running application instance. Shutting down.
But I could not have any access anymore through file manager or command-line. There were numerous different processes running by cryptomator and reboot was the fastest way to get system back.
This is good but is not a solution (more like a workaround) as all opened files will lose the connection and data loss may occur - there is never known when gvfs freeze occur and unsaved data will be lost. Also files are needed to reopen and over dav:// it is not so comfortable (fast) either.