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The problem is that "Search for updates to the currently installed features" is really slow, because it searches for updates to all features. So instead some users (like me and a few other Mylar users I know of) regularly use "Search for new features..", which does allow update sites to search to be specified. With weekly releases this results in a lot of disabled features, which are a pain to eventually uninstall because they aren't grouped and require two Eclipse restarts. So this seems like a usability bug that should be straightforward to fix by adding the update site search page to the option.
I agree it should definetly be possible to select the update sites that should be searched for. A simple "Select All" "Deselect All" and maybe "Inverse Select" would make the whole search for updates a lot more usable. This has also the nice benefit of being able to update a feature / plugin from another update site than specified in the plugin.xml by simply enabling the edit option in the choose updatesite pane.
"to update a feature / plugin from another update site than specified in the plugin.xml": you can use update policy file to do this
The policy feature seems suitable for organizations and for the case where you don't want to change the policy often. What the description of this report is asking for here is a simple addition to the UI so that the user could determine which update sites will be searched for this update. There are times when you'll want all of them to be searched. But if you're updating a single feature often, you'll just want to search that update site some of the time. The underlying issue here is that it can take minutes to search for updates to the SDK, which happens by default, whereas it takes seconds to search for updates for a particular feature that's also hosted on eclipse.org. So if for some reason the Eclipse SDK update check got 10x faster this would probably become a non-issue for most cases.
Bug 86593 tells a workaround: via Help > Software Updates > Manage Configuration, you can scan for updates of a specific feature. This currently only finds minor updates by default, see bug 82301.
Now that "Search for updates.." should work properly (bug 132450) I'm not sure if this feature request has any priority. I'm happy having it resolved as WONTFIX. Users can still vote for it if they find that they need it now that they can reliably start using "Search for updates".
The Eclipse Update component is no longer under development, and no longer exists in the Eclipse Platform 4.x stream. If this problem still occurs in Eclipse Platform 4.2 or later, please enter a new bug report against Equinox p2.