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[native_assets_cli] Curate public classes (#2245)

This PR tries the curate the classes which are in the public API of `native_assets_cli.dart` and adds some documentation to them.

* `(Build|Link)(Input|Output)` refer to the hooks the are the input or output of.
* `Hook(Input|Output)` refer to the subclasses
* `(Build|Link|Hook)Config` refer to the input they are the config of.
* `XXXBuilder` refer to the class they build.
* `Builder|Linker` refer to the hooks they should be used in.
* `EncodedAsset` refers to protocol extensions for encoding/decoding
* `PackageMetadata|PackageUserDefines|PackageUserDefinesSource` refer to the classes where they are used.
* `ProtocolExtension` documents it's the specification for an extension of the base protocol.
* `AssetRouting|ToAppBundle|ToBuildHooks|ToLinkHook` refer to each other in the hook output.

Deprecated classes have been removed:

* `Metadata|Dependencies` these were no longer used since the `XXXBuilder` pattern.

Classes only used in `package:native_assets_builder` have been moved there:

* `Target`.

The Dart docs can be inspected by `pkgs/native_assets_cli$ dart doc .`.

TODOs:

* This PR does not yet curate extension types, extensions, and top level functions.
* This PR does not yet curate the `code_assets.dart` and `data_assets.dart` libraries.

Context:

* Work before splitting up the package: https://github.com/dart-lang/native/issues/999

16 of 16 new or added lines in 2 files covered. (100.0%)

8063 of 10356 relevant lines covered (77.86%)

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