Frankly, due to lack of code fences it’s all but impossible to tell what you’ve done, what the errors are, where posted files start and end, etc.
A “normal” runtime.cfg file will have a lot of stuff in it but everything will be commented out.
##################### LOCALE ####################
# The default language that should be used. If not specified, the system default locale is used.
# The ISO 639 alpha-2 or alpha-3 language code (if there is no alpha-2 one).
# Example: "en" (English), "de" (German), "ja" (Japanese), "kok" (Konkani)
#
#org.openhab.i18n:language=
# The region that should be used.
# ISO 3166 alpha-2 country code or UN M.49 numeric-3 area code.
# Example: "US" (United States), "DE" (Germany), "FR" (France), "029" (Caribbean)
#
#org.openhab.i18n:region=
################ PERSISTENCE ####################
# The persistence service to use if no other is specified.
#
#org.openhab.persistence:default=
################### AUDIO #######################
# This parameter defines the default audio source to use (if not set, the first available one will be used.
#
#org.openhab.audio:defaultSource=
# This parameter defines the default audio sink to use (if not set, the first available one will be used.
#
#org.openhab.audio:defaultSink=
##################### VOICE #####################
# This parameter defines the default text-to-speech service to use (if not set, the first available one will be used.
#
#org.openhab.voice:defaultTTS=
# This parameter defines the default speech-to-text service to use (if not set, the first available one will be used.
#
#org.openhab.voice:defaultSTT=
# The default voice to use if no specific TTS service or voice is specified.
#
#org.openhab.voice:defaultVoice=
# The default human language interpreter to use if no other is specified.
#
#org.openhab.voice:defaultHLI=
################### EPHEMERIS ###################
# This parameter defines the default list of usual non workable days for the Ephemeris service.
# The value has to be surrounded by square brackets ('[' and ']') and optionally contain value delimiters - a comma ',' to be interpreted as a list of values.
# Example: [SATURDAY,SUNDAY]
#
org.openhab.ephemeris:dayset-weekend=[SATURDAY,SUNDAY]
# This parameter defines the default list of usual workable days for the Ephemeris service.
# The value has to be surrounded by square brackets ('[' and ']') and optionally contain value delimiters - a comma ',' to be interpreted as a list of values.
#
org.openhab.ephemeris:dayset-school=[MONDAY,TUESDAY,WEDNESDAY,THURSDAY,FRIDAY]
################ MISCELLANOUS ###################
# The karaf sshHost parameter configures the bind address for the ssh login to karaf.
# Default is 127.0.0.1 (localhost), so it is only possible to login from the local machine.
#
# Setting this to the address of another network interfaces will allow login from this network.
# Setting this to 0.0.0.0 will allow login from all network interfaces.
#
# !!! Security warning !!!
# Remember to change default login/password, if you allow external login.
# See https://www.openhab.org/docs/administration/console.html for details.
#
#org.apache.karaf.shell:sshHost = 0.0.0.0
# Setting this to true will automatically approve all inbox entries and create Things for them,
# so that they are immediately available in the system (default is false)
#
#org.openhab.inbox:autoApprove=true
# This setting allows to switch between a "simple" and an "advanced" mode for item management.
# In simple mode (autoLinks=true), links and their according items are automatically created for new Things.
# In advanced mode (autoLinks=false), the user has the full control about which items channels are linked to.
# Existing links will remain untouched. (default is true)
#
#org.openhab.links:autoLinks=false
If there is anything not commented out in that file, it’s there because you put it there. And of course, if you’ve put something in that file, the apt upgrade isn’t going to remove it.
I see no error messages posted above. I see notification that the runtime.cfg file contained changes made by you so the apt upgrade did not replace that file with the distro version of the file. That’s not an error. That’s just information.
That’s not rubbish. Thats probably stuff left over from OH 2 or it stuff added by openHABian.
The “rubbish” is adding new “tiles” to PaperUI’s “home” page to open other URLs not part of openHAB. If MainUI uses these, this is how you add to the “Other Apps” menu at the upper right of the Overview page.
You can delete them or even delete the whole file. If these are used by MainUI it won’t be no impact. It will remove entries in “Other Apps” that point to various openHAB docs pages and Frontail.
Again, it was never an error in the first place. If you or anything else has modified any file under services, apt is not going to replace those and remove your changes and it’s going to tell you so. Everything is behaving as it should.