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Don't blow away package manifest when updating
When we read a package manifest, we need a representation of the manifest that we can make reliable assumptions about. To do this, we disregard fields that we don't care about and we fill in default values for fields that we _do_ care about but haven't been explicitly provided. The problem is that when updating the version of a package, we are using a modified version of this representation of the manifest. That isn't good, because it means that the package's manifest ends up getting fundamentally changed. This commit fixes this by storing the original representation of the manifest when it is read. This representation is then used when the version is updated instead of the "parsed" representation. This does make the parsed representation immediately out of date, but that doesn't really matter.
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