fix: metadata on documents are orphaned

[JohnJyong]

Summary

1. add old metadata migrate command
2. remove old doc-metadata logic in service api

Tip

Close issue syntax: Fixes #<issue number> or Resolves #<issue number>, see documentation for more details.
fix #16256

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Checklist

Important

Please review the checklist below before submitting your pull request.

• This change requires a documentation update, included: Dify Document
• I understand that this PR may be closed in case there was no previous discussion or issues. (This doesn't apply to typos!)
• I've added a test for each change that was introduced, and I tried as much as possible to make a single atomic change.
• I've updated the documentation accordingly.
• I ran dev/reformat(backend) and cd web && npx lint-staged(frontend) to appease the lint gods

[DavideDelbianco]

From the source code of this PR it seems to me that there's no filtering logic for the built-in metadata keys

Those keys were/are present in the doc_metadata field

And the UI seems to throw an error when you attempt to add a custom metadata key that's already part of the built-in ones