Return the correct manifest for a JarFile create from a nested directory
Previously, if a JarFile was created from a directory nested inside another jar file, it would look for the manifest in pathFromRoot/META-INF/MANIFEST.MF. This is incorrect as, unlike a JarFile created from a jar file, the archives are one and the same so the manifests should be too. This commit updates JarFile so that its aware of how it was created (direct from a file, from a nested directory, from a nested jar). If it was created from a file or from a nested jar, it uses its manifest. If it was created from a nested directory, it uses the manifest of the root archive. Closes gh-5609
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