What config file can "application links" be modified from. The goal is to be able to remove and link applications through a config file instead of the application or REST.
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Simple answer is "none". Application links are held in the database, not files.
From memory, the only way you can write the details of a link into the database correctly is by copying the encoded stuff from an existing working link, which predicates that you'll have to have set it up via the UI or REST before.
Yes, they are.
If you modify them in the database, you'll have two problems.
1. As I said, you won't actually know what to put in there (unless you've copied it from an existing correctly configured link)
2. Exactly as @Joshua Sneed _ Contegix says, most (all?) Atlassian applications load and cache their links at startup. So if you poked new data into the database, you would need to restart them to make it re-read for the new data.
The SQL we use in Data Center is
select property_key, propertyvalue, propertystring.id from propertyentry join propertystring on propertyentry.id = propertystring.id where property_key like 'applinks.admin%url';
Then once we know the two ids 123, 234
update propertystring SET propertyvalue = 'https://my-other-wiki.example.com' where id in (123,234);
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