Introduce hidden `--overwrite-json` flag

[Poitrin]

WHY are these changes introduced?

Part of https://github.com/Shopify/internal-cli-foundations/issues/509 Is required by https://github.com/Shopify/cli/pull/1169

Issue https://github.com/Shopify/shopify-cli/issues/2433 was fixed with https://github.com/Shopify/shopify-cli/pull/2463. With https://github.com/Shopify/cli/pull/1169, Node CLI needs to pass Ruby CLI a hidden flag to differentiate themes created at runtime.

WHAT is this pull request doing?

Introduces --overwrite-json flag that Node CLI can pass to Ruby CLI.

How to test your changes?

1. In lib/shopify_cli/theme/theme.rb, remove the line @created_at_runtime = true, because theme will already have been created by Node CLI.
2. Make sure that your current store has 0 development themes.
3. Execute shopify(-dev) theme serve /path/to/theme --theme-editor-sync
4. Verify that CLI asks "Keep the remote version".
5. Exit the prompt.
6. Delete the development theme that has been created.
7. Execute shopify(-dev) theme serve /path/to/theme --theme-editor-sync --overwrite-json
8. Verify that CLI does not display any prompt.

Post-release steps

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Update checklist

• [x] I've added a CHANGELOG entry for this PR (if the change is public-facing)
• [x] I've considered possible cross-platform impacts (Mac, Linux, Windows).
• [x] I've left the version number as is (we'll handle incrementing this when releasing).
• [x] I've included any post-release steps in the section above (if needed).