Add pyrefly type checking: pyrefly.toml config, CI integration

[vfdev-5]

!!! PR based on #5460

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[vfdev-5]

This prevents pyrefly ignore comment on the code below:

out = dot_general(
      inputs,  # pyrefly: ignore [bad-argument-type]
      kernel,  # pyrefly: ignore [bad-argument-type]
      ((axis, contract_ind), (batch_dims, batch_ind)),
      precision=self.precision,
    )

and pyrefly is right on as self.promote_dtype output type hint is Array | None, so they deduce that inputs and kernel can be also None.

[vfdev-5]

Right now the check runs over single file to show that there is no more errors like # pyrefly: ignore [bad-class-definition] (as in previous attempt: https://github.com/google/flax/pull/5437/changes#diff-cfcdd6089c08daca13a27f79e07b856585c5f9b6910570f9cc3e7be76fd746b1R103)