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refactor: lake: manifest semver & code cleanup (#4083)
Switches the manifest format to use `major.minor.patch` semantic versions. Major version increments indicate breaking changes (e.g., new required fields and semantic changes to existing fields). Minor version increments (after `0.x`) indicate backwards-compatible extensions (e.g., adding optional fields, removing fields). This change is backwards compatible. Lake will still successfully read old manifest with numeric versions. It will treat the numeric version `N` as semantic version `0.N.0`. Lake will also accept manifest versions with `-` suffixes (e.g., `x.y.z-foo`) and then ignore the suffix. This change also includes the general cleanup/refactoring of the manifest code and data structures that was part of #3174.
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