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I think it would be a very good idea to make working sets more flexible/more dynamic... Scenario 1: My workspace currently contains 70 projects, half of it being projects containing unit tests. Per definition, all the test projects are named *.tests. Having the possiblity for working sets to include/exclude projects named *.tests would be a nice enhancement to my development experience (regular expressions would be greatly appreciated :) ) Scenario 2: The SCM I am using has the notion of "Changelists". I would like to write an extension for a workingset that dynamically includes all the files in a specific changelists. I don't think that is easily possible at the moment.
For scenario 1 you should use filters. Note that the Navigator does not support user defined filters at this point. Bug 1970 is requesting this feature for the Navigator. You can support scenario 2 by writing an extension to the org.eclipse.ui.workingSets extension point. You would listen to changes to the changelist and update the working set accordingly. Whenever the working set is changed you would send the CHANGE_WORKING_SET_CONTENT_CHANGE property change event (in IWorkingSetManager). Let me know if this works for you.
Closing, assuming you are happy with using filters for scenario 1 and that the path to solving scenario 2 worked.