In the new version what previously was only command line / console is now seems by default invokes some JLink GUI server and causes unwanted Window popups.

What is the proper way to disable this behavior, and keep to the old proper console only app as it always was?

The only non-proper - as I see, because you modifying install - option is to remove all execute permissions on that GUI Server app.

The GUI constantly interferes with operation - starting with asking to update firmware.

Passing exec SuppressControlPanel doesn't work; Requires to further pass exec SupressInfoUpdateFW.

One would hope that, passing above two, and then doing exec SilentUpdateFW, would avoid the GUI , but NO. .. While updating it yet another dialog pops up with progress...

How to avoid all these windows ..?

Because this was new JLink software, on the first JLinkExe run immediately FW update dialog popped up, which thus started this thread.
I immediately killed the app, and starting looking into how I can avoid these dialogs.

My setup is Linux x86_64 (Fedora based).

Thus the first thing I want: how to suppress this update dialog _immediately_ before you can do anything else - that is, before it (JLink) even thinks to pop-up anything. Thus I tried to pass this as commands to be executed - on startup.
That would at least suppress initial dialog, BUT, it also suppresses the check for firmware update ? (Why...? Why do I need a GUI dialog to check my firmware version?) How can I check within JLinkExe command shell inside, if firmware needs to be udpated, without GUI?

Secondly, I replaced SupressInfoUpdateFW - as Ideally i do want to update - with SilentUpdateFW, in the above command line. Then I got immediately another un-wanted behavior as i originally wrote: that, the dialog / progress bar window pop-up appeared showing me the progress. I do not want this, at all.

Not only that this progress bar in window is unnecessary - JlinkExe previously was working absolutely fine without this - it has problems to actually performing update correctly fully: after initial firmware updated, JLink seems gets re-set (I'm assuming), and drops out from USB connection and is suppose to reconnect. On my system, this dialog cannot handle this properly : after the JLink drops out , gets dropped back, the GUI window gets confused and tells me something along the lines update failed , or in bootloader mode, and basically bails - cannot proceed further. This is not a sane behavior by any means, it broke my JLink smooth usage.
But ignore that udpate window entirely - i know I can update as before if I just don't use it (as I wrote, I can prevent your GUI server from running, and then JLinkExe will "fix" broken update for me smoothly).

Could you PLEASE, please revert to a more sensible version of your _command_ line version of JLinkExe where one does not even have to set any flag to begin with to make it work as before? Could you make this the default, and rather add "-gui" flag to it? Or , add "-nogui" as you seems have on GDBServer?

Is this a new requirement, that you _have_ to start it without J-Link connected? I never for years did this before, as my JLink is connected before I start doing any work. Again, if this is new, I would rather you roll back to old method.
For test, start with Jlink connected, Then start your JlinkExe

But this sounds excellent. Thank you

So as to set a reminder to upgrade : which release number / version will be next ?

(Btw, Linux is what all embedded sw dev work must be on ^__^ )

I tried it, and the problem now was the Accept License terms dialog / message box.

Firmware update window suppression worked.