I'm a big fan of SonarQube as a developer. This time though I need to do admin work since I need to configure it from a fresh install. I see this rule in SonarQube "Methods should not have too many lines" but I don't see that it belongs to any of the default profiles ("FindBugs+FB-Contrib", "Sonar Way"). I think that's the reason I don't see any rule violations of this type from any of the projects. I thought this should be part of a common default profile since this is a pretty common violation. How can I add this rule to the profile? There are other rules that I need to add which I expected also to be in the default/available profiles already.
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You can't edit built-in profiles. Instead, you'll have to create a new profile, and then you'll be able to edit the rules to your heart's content. I suggest you initialize your new profile either by copying the rules from the built-in profile of your choice, or by inheriting from that profile. Note that choosing the latter means your profile can (and probably will) be updated by upgrading your analyzers; each new version of SonarJava, for instance, implements new rules and many of them are added to the Sonar way profile.