Make gorefs.yaml the source of truth instead of Markdown files

[pkalita-lbl]

To be done after #2232.

• Run the Markdown-to-YAML script for the last time. Move the updated gorefs.yaml file up one level to be a direct child of the metadata directory alongside other metadata YAML files. This file should now be treated as the source of truth and not the Markdown files.
• Move the associated LinkML schema up to the metadata directory and rename it gorefs.schema.yaml to align with existing metadata schema files.