I am trying to setup a project template or using REST give my users a function to create their projects with a bunch of configuration setup for them.
I cannot seem to find any way to set the issue type scheme or to set the issue types for a new project.
Take a look at createmeta
Returns a list of projects and the issue types that are associated with them.
Based on that information, filter out what is required (i.e. show only issue types for project X)
I don't believe updating a project's issue type is currently supported. Refer to this open ticket https://jira.atlassian.com/browse/JRASERVER-59948
This will need to be done manually via the Administration UI.
One thing I can suggest is to just associate all the available issue types to this project. That way you're able to create the issues via REST without any problems.
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