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I guess the simple answer to my example would be to set the 'Parsing Schema' during import/install to be the schema where the main application data / objects live.
However, our application (not APEX) uses multiple different schemas on the same database - and I want to report on (and manage) data across them all. I guess in this scenario the only approach is to adopt a dedicated 'Parsing Schema', grant privileges on all the necessary objects in each of the other schemas to the 'Parsing Schema', and then create synonyms for each of the objects in the 'Parsing Schema'. This way, the APEX Application itself is agnostic of the schema names in each environment.
There are other environmental values that my APEX application might need, such as the hostnames of servers that it may need to access, which I assume I would need to store in a pre-populated bespoke 'Application Configuration' table in the 'Parsing Schema' which I look up and use at runtime.
However, how would I define something like the LDAP Server (and credentials) that my APEX application uses to Authenticate against - when using the bundled LDAP Authentication Scheme, for example ?