Remove package.xml from partially-retrieved metadata before comparison

The package.xml manifest that's supplied when metadata is retrieved is the echoed back in the retrieve results. For partial retrievals, this can lead to confusion and potentially destructive changes when comparing retrieved metadata to local source as the partially-specified manifest from the retrieval response won't match the authoritative definition in the local source root.

To avoid this confusion, the retrieve response's package.xml file should only be included for comparison when performing a full retrieve for a module's contents, not a partial retrieve.

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