Clean-up SPIM JSON file

It is bids-compliant but has alot of intermediate gunk (e.g. the tile transformations)..

Could consider keeping the intermediate metadata.json file as a temp file, then having a rule that cleans it up downstream..

Start by inspecting the SPIM JSON output and the intermediate metadata.json file mentioned in the issue, then trace the workflow rule that produces them. Confirm which fields are intermediate tile transformations, preserve BIDS compliance, and verify that temporary metadata is cleaned up downstream without removing required output.

Written by the indexing model from the issue text.