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If I define two IApplications in two separate bundles, then start one of them with eclipse -console -application, I cannot see the other (with apps/startApp/activeApps). If I start up eclipse -console, I can see neither of them. It seems that what's happening is that the only IApplicationHandles that are being registered are those contributed by extension points in the bundle that contains the application listed in -application. Clearly, Eclipse knows where they are (because I can run -application on either) but the Equinox console seems to be blinkered depending on which one you started. Other apps in the same bundle are visible with activeApps. I'd have expected to see a full list of IApplications in the Equinox console, as long as those bundles are installed (or started). That doesn't seem to be the case.
See the runtime option "eclipse.application.registerDescriptors" in the help. Setting "eclipse.application.registerDescriptors=true" in the config.ini will show all applications, not just the default one specified in -application.
Fair enough.
NB the default application args set by PDE supplies -Declipse.ignoreApp=true. With that, no apps get started either. (Just in case anyone else finds this bug)