I did run into that issue and started eclipse one time from the command line with the -clearPersistedState flag. I had no idea at the time that would make that flag permanent.
I have been able to get Eclipse to retain changes to my workspace ONLY if I start it on a command line with the -persistState flag set to true (./eclipse -persistState true). If I start it from the icon on my mac then any changes to the eclipse workspace do not get saved between starts of eclipse.
I did try to add the -persistState true flag to the eclipse.ini file but it has no effect there.
Maybe I am the only one, but I cannot find a way to update to this version. I am a novice with Eclipse. Any detail on how to update to this latest release?
Thanks.
Started having the glassfish issue again (macbook pro). Adding these 2 lines to the config.ini fixed it for me.
btw, On the mac you have to open the folder containing eclipse then right click and select "Show Package Contents" to see the /Contents/Eclipse/configuration/config.ini