If Mylyn bundles cannot be run under Felix, then the IDE should offer a standard build target to run Equinox.
The following seems to work:
java -Declipse.ignoreApp=true -Dosgi.bundles=file:...org.eclipse.core.contenttype-*.jar,file:...org.eclipse.core.jobs-*.jar,file:...org.eclipse.core.net-*.jar,file:...org.eclipse.core.runtime-*.jar@:start,file:...org.eclipse.core.runtime.compatibility.auth-*.jar,file:...org.eclipse.equinox.app-*.jar,file:...org.eclipse.equinox.common-*.jar,file:...org.eclipse.equinox.preferences-*.jar,file:...org.eclipse.equinox.registry-*.jar,file:...org.eclipse.equinox.security-*.jar,file:...org.netbeans.core.osgi-*.jar@:start,file:...org.netbeans.core.startup-*.jar@:start,file:...org.netbeans.bootstrap-*.jar@:start,file:...org.openide.modules-*.jar@:start,file:...org.openide.util-*.jar@:start,file:...org.openide.util.lookup-*.jar@:start,file:...org.openide.filesystems-*.jar@:start -jar ...org.eclipse.osgi-*.jar -consoleLog
Integrated into 'main-golden', will be available in build *201205010400* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress)
User: Jesse Glick <firstname.lastname@example.org>
Log: #211809 amelioration: do not even copy org.eclipse.osgi.jar to bundles area.
(Netbinox was already excluded, but it seems modules/ext/*.jar get scanned too.)
This means that Mylyn and similar bundles are just not started.
The effect is a few warnings on console and Bugzilla support is missing.
Better than trying to start all these bundles but throw confusing CCEs.
No plans to work on it anytime soon.