Privatize several members on PackageGraph

[srawlins]

• Privatize PackageGraph.documentedPackages, PackageGraph.invisibleAnnotations,
• Remove Package.publicLibraries, just inline into one call site.
• Remove PackageGraph.sdk, which was only used to initialize sdkLibrarySources, and PackageGraph.allCanonicalModelElements, inlining into the one call site.
• Initialize sdkLibrarySources in the constructor.

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