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Adjust to JavaCore.defaultRootModules deprecation #1958

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Use the new method that filters based on the release. If release option is not set, use target and if it's not there too use the latest version.

Use the new method that filters based on the release. If release option
is not set, use target and if it's not there too use the latest version.
@akurtakov
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@stephan-herrmann As this is continuation of eclipse-jdt/eclipse.jdt.core#2786 (in a way), would you please review?

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