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.

2. 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

3. 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)

4. 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
   

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