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[hooks_runner] Rerun hooks if outputs are deleted (#3358)

Bug:

* https://github.com/flutter/flutter/issues/186305

The hooks_runner was not rerunning hooks if output files got deleted. Only if dependencies got deleted.
Most of the build hooks would only output to locations that users would not delete (e.g. `input.outputDirectoryShared.resolve(...)`. However, users might output to `input.packageRoot.resolve(...)` and delete files manually. This is a bad idea, because you'd write to the pub cache if your package is used as a dependency from pub! However, users might do this. And they might do this for packages/apps that are not published. So we should fix this.

Because the hooks runner doesn't know what output files are, we need to add this to the `ProtocolExtension` so that every extension can provide the right information. This means a breaking change to `package:hooks`. v2 here we come. (Open to alternative suggestions.)

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