Arrangement of apps whether on home screen or in app drawer is part of app data of launcher app. If your launcher app doesn't offer support for Import/Export of user settings, than try using adb to backup your launcher app's data. Verify the backup and see whether the user settings were indeed backed up not.
If adb solution is not useful than the only way ...
If you want to execute an adb pull comand and at the same time monitor the on-device log via adb logcat you can do so by executing each command individually in it's own terminal/cmd.exe instance.
adb is not limited to a single connection (as the MTP protocol is). Hence you can execute two or more adb command simultaneously. Even multiple adb push or pull ...
Just pulling all files via adb to a WIndows computer has multiple problems:
Android/Linux allows multiple files in one directory that just differ in their case.
The file-system on Linux allow characters in file- and directory names that are disallowed on Windows
Some file-names are completely disallowed on Windows which are just regular file-names on Linux/...
Try replacing the sim to a different phone and downloading whatsapp in it. Log into the whatsapp with your phone number. It will prompt to retrieve saved data. Make sure you retrieve it otherwise it will be difficult. Whatsapp automatically backs-up the chats.
FWIW, On a Motorola G3Turbo with Android 6.0, and:
Android Debug Bridge version 1.0.41
I had to use quotes in a rather... weird way:
./adb -d backup "-all" "-system" "-shared" "-apk" -f <filename>
Which should have been absolutely the same as no quotes at all. Since this really, really should have been the same ...
I had problems with this too, and today finally it worked. Unfortunately I'm not sure which of the following additional steps did the trick, but maybe it helps others:
I copied the entire WhatsApp folder over from the old phone to the new one (zipped it using Total Commander, copied it to a PC via USB, copied it to the new phone also via USB, unzipped it ...