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Stapler plugins are available for both NetBeans and IntelliJ. Either are well supported for Jenkins plugin development. Eclipse is not well supported.
I did not write CpsScriptTest but perhaps Kohsuke Kawaguchi can take a look at that failure. Anyway, a single test failure is not much cause for concern, when there are a number of tests that fail on occasion, perhaps due to race conditions. You can just file a pull request and a Jenkins builder will automatically run all tests against your changes and report any failures, which plugin maintainers would evaluate to see if they are significant or not. I rarely run all tests in the Workflow plugin myself, as it would take much too long; I would only run tests I think might be related to changes I am making.
~/.jenkins/cache/ is JENKINS-18578.
For Workflow, hpi:run should be run inside aggregator, which from NetBeans you can do via just pressing Run Project when you have the Jenkins developer plugin installed: https://github.com/jenkinsci/workflow-plugin/blob/master/README.md#source-organization
By the way, if you are unfamiliar with Jenkins development, I will warn you that many (though not all) parts of Workflow are especially tough to get into, compared to most other Jenkins plugins.