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I recently updated eclipse to the latest Oxygen version.

I don't really mind much if I am not using the latest version of each software, but whenever eclipse prompts me to update something, I go ahead and accept it as I trust it knows what it's doing. Since I have some plugins installed and since I've had eclipse for quite some time, I have a long list of software sites listed in my Install/Update preference pane.

Lately some of these sites seem to have stopped responding, so I removed them from the list. Upon clicking on help > check for updates however, they simply come back to the list.

Could someone explain to me why this keeps happening and why I am unable to control what eclipse is contacting?

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An installed feature can contribute an Update Site if they want. Your best bet is to leave them there, but disabled.

http://help.eclipse.org/oxygen/topic/org.eclipse.platform.doc.isv/reference/misc/feature_manifest.html?cp=2_1_5_20

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