At the moment the fact is that despite the old FITS usage and the recommendation in the WCS document many file from camera are top-down.
This the case at least for the two I can test, indi_gphoto that return the FITS rows in the same order than libraw and for indi_atik from the Atik SDK. This is probably also the case when using other manufacturer SDK.
But it is not necessary to change the way the data are written to the file because this can affect the performance. So probably no alignment code need to be changed.
The idea with adding this new ROWORDER keyword is to clarify the way the processing software treat the image specifically with bayer matrix. All of this with minimal change in the capture software.
So if a driver know the camera return data in top down order it just add ROWORDER = 'TOP-DOWN' in the header, ROWORDER = 'BOTTOM-UP' in the other case.
Redhat server is really not intended for this use, as you remarked many required packages are not available on this system.
A good start is to install EPEL which add many packages from Fedora to Redhat server:
Then for everything else that is missing you need to install from source. This can be a big work to solve all the dependencies and even more work to maintain.
The interest of Astroberry is to not have to do this kind of operation, but if you really need it the phd2 build instruction are here:
The yellow background for the top message is probably because of an incomplete dark theme because the color is not fixed in code.
For me using the Gnome standard theme Adwaita-dark the message background is dark gray. This theme for Gtk2 is normally available in the package gnome-themes-extra-data.
I just submit a fix for the original issue with the 3 polar alignment tools.
It is possible to set a dark theme for phd2 without any change in Ekos because phd2 use the Gtk theme and Ekos the Qt theme. Be careful to not use a theme setting software that change both.
Also be careful that since Ubuntu 20.04 wxWidgets is no more packaged for Gtk2 but only for Gtk3. The phd2 ppa version for 20.04 is build for Gtk3 so this is the Gtk3 theme you now need to change.
No, PHD2 never set tracking because this is not it's job.
Set tracking on is part of the target centering operation, which include slewing to coordinates and ensuring the mount stay there. This is a requirement before to start guiding.
PHD2 use the properties TELESCOPE_TIMED_GUIDE_NS and TELESCOPE_TIMED_GUIDE_WE for the guide command.
You can try them directly without PHD2 in the INDI "Motion Control" tab, the label is "Guide N/S" and Guide E/W".
Activate the INDI driver debug log, this must show message like this with the PHD2 manual guide:
13:38:53.305: [DEBUG] Timed guide South 750 ms at rate 7.52053
13:38:53.305: [DEBUG] StartDETracking() : trackspeed = -7.52053 arcsecs/s, computed rate = -0.5
13:38:53.305: [DEBUG] SetDERate() : rate = -0.5
13:38:54.056: [DEBUG] StartDETracking() : trackspeed = 0 arcsecs/s, computed rate = 0
13:38:54.566: [DEBUG] End Timed guide North/South
In your case StartDETracking() is in your modified skywatcher.cpp