I though that there should be an option to simply put a password on a directory and rename it something like .muttmailrc to make it look like a part of the system.

That is what 'gpg -c' does. You can use option -o to specify the name of the encrypted file. And, as chaosmonk told you, there is a Nautilus extension, seahorse-nautilus, to do that with the mouse, from GNOME's file manager, which I happen to use: right-click on the file/directory and choose "Encrypt..." in the contextual menu.

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