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070319. If you open the JDK util project and let it scan, it will (I think) scan just the Collections-related classes and then stop. Fine. Now open jarzip. Nothing new is scanned, even though this project has a new set of includes. For example, if you use Go to Type, JarFile is not offered (except from the bootstrap JDK), but HashMap is. Possible behaviors: (0) Do nothing, as now, i.e. this is WONTFIX. If you wanted to work on >1 project, you're out of luck: close project #1, shut down the IDE, delete var/cache/, restart, open project #2. (1) Detect the changed includes/excludes, throw out the old cache, and rescan. OK if you just want to switch from one project to the next, which is likely. (2) Scan those packages/classes which were not scanned before, i.e. extend the existing cache as needed.
In the point (0) it should be enough to close the first project. The problem is that RepositoryUpdater maintains the set of already scanned roots and the root of the old project is the same as a root of the new project => the RepositoryUpdater do not scan it again. For now I don't know any fast way how to find out that the root has different excludes, maybe ClassPath.SOURCE(oldRoot) != ClassPath.SOURCE (newRoot) will work. If it works it will behave like point (2).
Old TM. -> 6.0.
moving opened issues from TM <= 6.1 to TM=Dev
Two projects on the same source root are not supported, but on the other side the implementation described by Jesse in point (1) should be doable and may help.
Resolving all issues with milestone "future" as LATER. If you feel strongly that it should be implemented please reopen and set the target milestone to "next".
NetBeans.org Migration: changing resolution from LATER to WONTFIX