Don't blow away package manifest when updating version

[mcmire]

Currently, when updating the version for a package manifest, we do not do a good job of preserving the original version of the manifest. First, readManifestDependencyFields includes dependency fields that aren't in the original manifest, and second, readManifest only includes manifest fields that we care about and discards the rest. Obviously, this is no bueno, and we should fix this.