I had the same problem today after upgrading from Juno to Kepler. I solved it as follows:
Make a backup copy of the file:
eclipse\configuration\org.eclipse.equinox.simpleconfigurator\bundles.info
Then manually edit the source file, find and remove all duplicate packages. For each duplicate you find, save the number with the most recent version number. For instance. I had lines like:
org.eclipse.core.commands,3.6.1.v20120814-150512,plugins/org.eclipse.core.commands_3.6.1.v20120814-150512.jar,4,false org.eclipse.core.commands,3.6.100.v20130515-1857,plugins/org.eclipse.core.commands_3.6.100.v20130515-1857.jar,4,false
In this case, I deleted line 3.6.1 and saved line 3.6.10 . Be careful only to delete lines where the name before the first comma is identical.
After that, run Eclipse with the -clean flag and you should be up.
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