[air] update checkpoint.py to deal with metadata in conversion.

[xwjiang2010]

Why are these changes needed?

This is carved out from #25558.
tlrd: checkpoint.py current doesn't support the following

a. from fs to dict checkpoint;
b. drop some marker to dict checkpoint;
c. convert back to fs checkpoint;
d. convert back to dict checkpoint.
Assert that the marker should still be there

Related issue number

Checks

• I've run scripts/format.sh to lint the changes in this PR.
• I've included any doc changes needed for https://docs.ray.io/en/master/.
• I've made sure the tests are passing. Note that there might be a few flaky tests, see the recent failures at https://flakey-tests.ray.io/
• Testing Strategy
  • Unit tests
  • Release tests
  • This PR is not tested :(

[ericl]

Looks good as a short term fix. I think in the long term we should consider just storing everything in the same format (data == metadata), I don't think there's a great reason why data files aren't stored as separate dict keys.