Eli Zaretskii <eliz@gnu.org> writes:

>> One solution would be introducing separate  .desktop file
>> (i.e. 'etc/emacsclient-org-protocol.desktop'), analoguous to the already
>> existing 'etc/emacsclient-mail.desktop' (which uses '%u').
>
> Ihor, could you please look into this?

I am attaching an *untested* patch that implements a new .desktop file.
Note that an alternative could be handling file:// URIs by Emacs. Your call.

> (Each time such issues pop up, I regret again that we agreed to
> include these *.desktop files in our source tree, sigh.)

We are obliged to cooperate with other parts of GNU toolchain, don't we?