Try:

buildType.setOption(SBuildType.BT_CLEAN_BUILD, true);

If you want this option to be persisted, add this too:

buildType.getProject().persist();

"swabra.mode" and "swabra.after.build" are runner parameters (i.e. parameters which should be passed to build runner on the agent), to set them use:

buildType.addRunParameter(new SimpleParameter("swabra.mode", "true"));

BTW if Swabra plugin is enabled there is no need to set clean build option.

To update build number pattern use:

buildType.getBuildNumbers().setBuildNumberPattern(pattern)

buildType.getBuildNumbers().persist();

As for VcsTrigger - this is not a part of open API, and most likely will change in the future (in fact VcsTrigger API has already changed in 5.0). But if you really need it you can do the following:

// iterate over build type triggers and find jetbrains.buildServer.buildTriggers.vcs.VcsTrigger using instanceof

buildType.getBuildTriggers()

// use method setIncludeRules() to set collection of rules:

vcsTrigger.setIncludeRules(list<string>)

Note that this method is named differently in 5.0.

Do not forget to call persist after the settings change.