Is there an email client that is integrated with thebrain?
I'm using TheBrain on OpenSuse Linux, and I've found that integration has improved tremendously for me. I have been using various webmail products for the last few years (I've found it difficult and time-consuming to migrate my Kmail as I've upgraded over the years), so it will take a bit for me to get back to it, but I'd like to assist you when I get back in front of my Linux desktop this evening.
When you say that your system does not know how to open the akonadi message, do you mean that you are trying to open it within TheBrain as an attachment? Or is it that you are trying to open the attachment from the Thought folder that the email attachment is in, from the linux desktop? I'd recommend first making sure that your Linux environment can handle the file type properly, then proceed to getting it working with PB.
I've been trying to wrap my head around Akonadi for quite some time now, but I understand that things like messages and contacts are not actually stored in Akonadi, which serves as a pointer. KMail is still storing your mail.
Are you working in KDE and Plasma (that would be the default KDE configuration on a newer install). I'm curious to know what happens when you drag a link of a KMail message into a Dolphin or Konqueror folder. I think it might be important to distinguish between moving the message out of Kmail, versus creating a link to it. Is the result something that you can use to open the original message?
If so, then it is a matter of configuring TheBrain to invoke the correct command to pass the link to Kmail.