We need something more intuitive and permanent...
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It is important that you edit the mbdock.session file when X is not running, because X reads it at startup and writes it on shutdown, so modificatoins which you did while X is running are overwritten.
There may be a more intuitive way:
Once you found your prefered command line options, add them to the file /usr/share/applications/mb-applet-clock.desktop to the Exec line.
However, I am not sure if this will work, i.e. if these optoins will also be written automatically into the mbdock.session file on X shutdown.
However, if this works, you can remove and restart the clock applet as many times as you want without losing the options.
There is no more intuitive way to use command line options on applets, as far as I know.
If you need a GUI-based solution, one would have to rewrite the applet entirely, making it use a config file and a configuration menu, so it can be started without command line options.
If it turns out that using the .desktop file the options are not preserved either, it is still possible to write a wrapper script with the command line options, and et the .desktop file start that wrapper script instead of the actual binary.
I have a completely different solution:
I have created a copy of the mbdock.session file, configured that file to fit my needs, and added a command to the ~/.xinitrc script which always overwrites the mbdock.session file with my fixed copy.
That way, I can use whatever command line options I want,
I can edit that copy of the file always, even when under X,
BUT I lose the feature that I can permanently add and remove applets to / from the panel. I can add / remove tham for the running session, but as soon as I restart X, the configuration from the mbdock.session copy is restored.
Initially, I chose that method because some or all applets occasionally vanished (which is fixed now, I think). I had to re-start them manually, then restart X, to have them in the mbdock.session file again.
So I created that fixed configuration with my prefered applets and let xinitrc always use that one instead of the one saved on last X exit.
You see, there are a lot of options.
You just have to choose the one which has the most advantages and least disadvantages for you.
daniel