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Subsequent to an email discussion with Tomasz Slota, I am filing this bug as a reminder to address this by beta release. Currently we switch on verification for all project types. We should enable verification based on a project's module type. e.g. if a project does not use ejb 3.0, then don't waste any CPU by running ejb rules... It is tricky for persistence rules, because any Java project can use persistence. May be we should run, rules like NoPersistenceUnitFound every time and only if that succeeds, we should run rest of the persistence rules.
Tidying up before the beta release I am changing this issue type to 'enhancement', as it doesn't trouble the end user (currently we are meeting editor performance objectives). Sorting it out is still a high priority.
Obsolete milestone, please reevaluate