Fix crate IDs when multiple workspaces are loaded
Previously, we assumed that the crate numbers in a `rust-project.json` always matched the `CrateId` values in the crate graph. This isn't true when there are multiple workspaces, because the crate graphs are merged and the `CrateId` values in the merged graph are different.
This broke flycheck (see first commit), because we were unable to find the workspace when a file changed, so we every single flycheck, producing duplicate compilation errors.
Instead, use the crate root module path to look up the relevant flycheck. This makes `ProjectWorkspace::Json` consistenet with `ProjectWorkspace::Cargo`.
Also, define a separate JSON crate number type, to prevent bugs like this happening again.
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