Guys, an update to Pulse (version 2.4.2) went out yesterday and one of the enhancements was to no longer manage the underlying JRE’s cert store, so you should be able to make use of the standard
-Djavax.net.ssl.trustStore
-Djavax.net.ssl.trustStorePassword
arguments again to contribute certs to your MyEclipse installation. Please let us know how this goes for you.