Check Notebook Execution Freshness

Verify that all registered notebooks have been executed and their outputs are current.

Steps

1. Read _quarto.yml and extract all notebook paths from manuscript.notebooks.

1. For each registered notebook, check:

• Has outputs: Open the .ipynb JSON and check if any code cells have non-empty outputs arrays
• Last modified: File modification timestamp of the .ipynb
• Outputs age: Check execution metadata timestamps in cell metadata (if present) to determine when outputs were last generated
• Freeze cache: Check if _freeze/notebooks/<name>/ directory exists and contains cached output

1. Determine freshness status for each notebook:

• Current: has outputs and the .ipynb has not been modified since outputs were generated
• Stale: has outputs but the .ipynb source cells have been modified more recently than the outputs
• Unexecuted: no outputs in any code cell
• Freeze only: no cell outputs but a _freeze/ cache exists (Quarto will use the cache)

1. Report a summary table:

Notebook Has Outputs Last Modified Status ───────────────────────────────────────────────────────────────── notebook-01.ipynb Yes 2026-02-28 14:30 Current notebook-02.ipynb Yes 2026-03-01 09:15 Stale notebook-03.ipynb No 2026-02-25 11:00 Unexecuted

1. If any notebooks are stale or unexecuted, flag them and offer to run /project:execute to re-execute all notebooks.

1. If all notebooks are current, report "All notebooks are up to date."

Error handling

• If _quarto.yml has no notebooks registered, report "No notebooks found in _quarto.yml" and stop.
• If a registered notebook file does not exist on disk, flag it as missing.