Fix options overriding aad app manifest. Closes #3555

[martinlingstuyl]

Closes #3555

This PR fixes a bug where options would incorrectly override manifest properties:

• Manifest scopes where merged with the options, this is now changed: when options apisDelegated or apisApplication are specified, the manifest scopes and roles are ignored.
• the multitenant option will now override the manifest property
• the implicitFlow option will now override the manifest property
• the withSecret option will now no longer create two secrets when a manifest secret is present. It will not create the manifest secret.
• the custom scope and identifier uri options will now override the manifest scope and identifier uri.
• the certificate options will now override the manifest properties.

[milanholemans]

Hi @martinlingstuyl

Seems like you are getting some merge conflicts, could you resolve them please?

Thank you

[martinlingstuyl]

OK @waldekmastykarz, I fixed the comments!

[waldekmastykarz]

Merged manually. Thank you! 👏