I am attempting to append an environment to an existing deployment project, but when publishing the deployment the existing (manual) configured projects are being overwritten by environment(s) built by Bamboo Specs.
Is there any way to retrieve existing configuration to append an environment rather than requiring the entire deployment project to be built within Bamboo Specs?
Bamboo Specs are supposed to be complete source of truth about the object they represent, so no, there's no way to append something to an existing Bamboo object. You need to define the complete project, always.
What can you do however is to export your existing Deployment Project to Bamboo Specs and start from there. Simply go to configuration of your project and pick 'View project as Java Specs' from the menu in top right corner.
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