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Ignoring manifest.yml is an intentional design decision that I don't currently have plans to change.
I might consider adding an option to local.yml to use the environment variables from an app specified in manifest.yml. Is this a compelling option for your use case?
Our use case is to setup our deployment pipeline to trigger cf local and construct an unittest environment that is (almost) identical to the actual CF runtime environment and run the unittest before cf push.
Understand your design idea and your suggested enhancement will help. Originally I'm just thinking if cf local would follow the original manifest.yml by default, and override/supplement any additional options specified in local.yml that are specific for cf local usage, but it's okay if you want to prevent any potential confusions.