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I ended up in a situation where Mylyn was installed for free during other bundle installs. This was really confusing and checking the installation history I could not see a line with Mylyn. So I had no idea how Mylyn ended up being installed. After investigation, I found out that the your kit bundle has two optional dependencies on Mylyn Junit bundles. This pulls in all Mylyn when this bundle is installed, but the installation history doesn't mention Mylyn. I think the installation workflow could be improved by showing what bundles can be optionally installed and let the user decide which ones should be installed. After the installation, these optional installed bundles should be part of the installation history in order to be able to uninstall them if needed. This is really bad with 4.x in which Mylyn is causing lots of grief right now. So Mylyn should not be installed in a 4.x workspace as long as the bug 325392 is not fixed.
The general issue is being discussed in another bug. *** This bug has been marked as a duplicate of bug 247099 ***