Update CLI upgrade docs to reflect automatic migration

[mintlify]

Summary

• Updated installation.mdx and organize/settings.mdx to reflect that the mint upgrade command has been removed
• The CLI now automatically detects mint.json and converts it to docs.json when running mint dev, mint broken-links, or mint rename

Triggered by the latest package bump in mintlify/mint which includes the removal of the standalone mint upgrade command in favor of automatic migration.

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Note

Low Risk
Documentation-only changes that remove references to the deprecated mint upgrade command and describe automatic mint.json → docs.json conversion; no runtime code or behavioral changes.

Overview
Updates the CLI docs to reflect that config migration is now automatic: mint.json is converted to docs.json when running commands like mint dev, mint broken-links, or mint rename, removing the prior manual mint upgrade step.

Adjusts the upgrade steps in installation.mdx and organize/settings.mdx to instruct users to run any CLI command, then review the generated docs.json and delete mint.json after verification.

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[mintlify]

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[ethanpalm]

Closing as duplicate of #5049. That PR covers the same automatic mint.json → docs.json upgrade with broader file coverage and will be reviewed separately.