I think that there is a small parameter checking bug with SQLcl Projects (I think since version 25.4) related to the export.apex.expSupportingObjects configuration option.
TL;DR: the command parameter now only accepts lowercase letters (specifically “i”) while the actual config file requires it to be uppercase.
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Example command:
SQL> version
Oracle SQLDeveloper Command-Line (SQLcl) version: 25.4.2.0 build: 25.4.2.044.1837
SQL> project config set -name export.apex.expSupportingObjects -value I
ERROR: An error has occurred processing your request
ERROR:Invalid value supplied for export.apex.expSupportingObjects, valid values are y,n,i
SQL> project config set -name export.apex.expSupportingObjects -value i
Process completed successfully
SQL>
However, with "expSupportingObjects" : "i", in .dbtools/project.config.json, the supporting script objects are not included. (Which actually caused a problem for me.)
Workaround is simple: just change to uppercase "I" in the config file manually. And then supporting scripts do work/are included.
Consequently, I think that this is a small bug related to the value processing (checking) in the project config command.