Is there a way for Cryptomator to authenticate via SSH agent keys? This would be excellent for those who use auto-key-loading password managers like Keepass or Bitwarden.
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No. Cryptomator only accept (printable) passwords. But you can encode your ssh key with base32/base64 and use it as password 
There’s a plugin for storing vault’s password in KeePassXC purejava/keepassxc-cryptomator: Plug-in for Cryptomator to store vault passwords in KeePassXC.
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I use and recommend the keepass option.