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.

6. 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.