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Currently if one uses a different bundle root together with a autogenerated manifest (e.g. maven/bnd bundle plugin) it is quite hard to look at the outcome because output folder are hidden by default, thus one needs to enable to show then (what is mostly undesired), then navigate to the correct place (target/classes/meta-inf/manifest.mf in most cases). To make this more convenient, it would be really helpful if PDE would simply create a linked (eclipse) resource that points to the appropriate place.
That's a good suggestion. The hidden MANIFEST.MF bothered me too. In case it is hidden the whole META-INF folder could be linked into the root of the project. This would have the advantage, that it looks familiar like with the default bundle-root and one can see the other content of the META-INF as well. It could be done in the WorkspacePluginModelManager when a Plug-in model is created and it is detected that the META-INF folder is (effectively) hidden. I should only be ensured that the linked resource is deleted/refreshed if the bundle-roots is changed or the project is moved (and maybe also if it is closed/deleted). At the moment I working on completing my pending Gerrits to not be a barrier for PDE's move to GitHub, but I can take care of this once PDE has moved or if there is time left (I think the change should not be too big).