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So my iCloud setup is brokenly, apparently because an incomplete macOS Mojave upgrade (from High Sierra). How can I "re-upgrade" to (reinstall) Mojave without loosing my existing data (e.g. in /Users/) and applications (e.g. /Applications/Audio\ Hijack.app/)?
For instance, is Command + R on startup (then "Reinstall macOS") the right entry point, or can I just repeat the part of the installation that is concerned with iCloud?
Without knowing the root cause of your iCloud issues it‘s impossible to say what exactly will help to solve it. You can reinstall macOS Mojave from Recovery (Cmd-R), and there is an option to install it without deleting your data. Whether this will solve your issues remains to be determined. And, as far as I know, there is no way of rerunning just parts of the installation.
PS: As always making a backup of your data before upgrading is highly recommended.
/Applications/Audio\ Hijack.app/, or will I have to reinstall those? (And yes, backup exists.)
/Applications (e.g. /Applications/Utilities presumably belongs to it), or does it comprise only part of it (i.e. leave my third-party apps intact)? Third-party application folders are only part of the larger picture. What I am really wondering is whether Command + R with "reinstall the OS" part is the appropriate way forward. Thx your your help (and I hope you won't suggest just trying it given that there is a backup available :-)
In response to the original question: You can't just select parts of the system software to reinstall; you have to reinstall all of it but that shouldn't affect your mac.
To clarify about reinstalls/clean installs: As far as I know/can remember there isn't an "option" to just reinstall/repair install mac os. Apple actually make it simple - if you boot to recovery mode (hold command and r while restarting on mojave (especially with an apfs formatted drive- holding alt down to select the recovery drive doesn't display the recovery drive to select it anymore)). When the screen loads up and you select install mac os, if you select your drive with an existing install of mac os on then it will just reinstall the system files (including ONLY the apple software (terminal, textedit, iTunes, etc) BUT won't touch your data files, user accounts or the applications that you installed yourself and they should work as before).
IF you want to do a clean install (removing all of your own data and applications) you must first select disk utility, select your drive and erase it/format it. THEN it will install just the mac os and everything will be like factory default settings.
!!! aha !!! I finally fixed this from the Terminal:
defaults delete com.apple.iTunes MacBuddyStoreID
Now iCloud has stopped complaining about my partially set up iCloud account.
probably got set when I migrated my account.
The way I tracked this down was by entering these commands:
defaults read > ~/defaultsDump.txt
edit ~/defaultsDump.txt
(Note: for me, this creates a huge 30MB text file.)
then searched ~/defaultsDump.txt for my email address that iCloud somehow got a hold of.
Found the MacBuddyStoreID in com.apple.iTunes!
EDIT My defaultsDump.txt also reveals that 2 different email addresses are involved. It also pointed me towards a problem in my Keychain after migrating. I think I've completely solved it now, by deleting ancient keys for an old email address from Keychain Access.app
repeat the part of the installation that is concerned with iCloud