I ran into an issue w/ removing the existing dependencies from a plan. The blow is the error message that I got from the publish attempt:
2018-05-29 16:43:19,817 INFO [BambooServer] An error occurred while publishing plan UIWEB-WEBMASTERTESTSCYLLA: Plan import is blocked to prevent deleting your plan dependencies silently. If you are confident that you want to delete all plan dependencies, use com.atlassian.bamboo.specs.api.builders.plan.Plan.noDependencies method explicitly.
So I tried to use noDependencies() method but didn't work because it's deprecated. Is there any workaround solution for removing a dependency from an existing plan other than noDependencies()?