rustc_metadata: Privatize more things

Continuation of https://github.com/rust-lang/rust/pull/66056.

The most notable change here is that `CrateMetadata` is moved from `cstore.rs` to `decoder.rs`.
Most of uses of `CrateMetadata` fields are in the decoder and uses of `root: CrateRoot` and other fields are so intertwined with each other that it would be hard to move a part of them into `cstore.rs` to privatize `CrateMetadata` fields, so we are going the other way round.

`cstore.rs` can probably be dismantled now, but I'll leave this to some other day.
Similarly, remaining `CrateMetadata` fields can be privatized by introducing some getter/setter methods, but not today.

r? @EddyB