Add notes on error-tolerant execution to CLI docs

docs/using-cli.md

@@ -26,18 +26,6 @@ jupytext --set-formats ipynb,py notebook.ipynb  # Turn notebook.ipynb into a pai
 jupytext --sync notebook.ipynb                  # Update whichever of notebook.ipynb/notebook.py is outdated
 ```
 
-For convenience, when creating a notebook from text you can execute it:
-```bash
-jupytext --set-kernel - notebook.md             # create a YAML header with kernel metadata matching the current python executable
-jupytext --set-formats md:myst notebook.md      # create a YAML header with an explicit jupytext format
-jupytext --to notebook --execute notebook.md    # convert notebook.md to an .ipynb file and run it
-```
-
-If you wanted to convert a collection of Markdown files to paired notebooks, and execute them in the current Python environment, you could run:
-```bash
-jupytext --set-formats ipynb,md --execute *.md
-```
-
 You may also find useful to `--pipe` the text representation of a notebook into tools like `black`:
 ```bash
 jupytext --sync --pipe black notebook.ipynb    # read most recent version of notebook, reformat with black, save
@@ -58,6 +46,37 @@ Note also that on Windows you need to use double quotes instead of single quotes
 
 Execute `jupytext --help` to access the full documentation.
 
+### Execute notebook cells
+
+For convenience, when creating a notebook from text you can execute it:
+
+```bash
+jupytext --set-kernel - notebook.md             # create a YAML header with kernel metadata matching the current python executable
+jupytext --set-formats md:myst notebook.md      # create a YAML header with an explicit jupytext format
+jupytext --to notebook --execute notebook.md    # convert notebook.md to an .ipynb file and run it
+```
+
+If you wanted to convert a collection of Markdown files to paired notebooks, and execute them in the current Python environment, you could run:
+```bash
+jupytext --set-formats ipynb,md --execute *.md
+```
+
+Please note: if any notebook cell errors, execution will terminate and `jupytext` will not save the notebook. This can cause headaches as the details of any error would be encoded in the notebook that isn't saved. But there's a way: `jupyter nbconvert` has a mode which will still save a notebook if a cell errors, producing something akin to what would happen if you ran all cells manually in Jupyter's notebook UI.
+
+```bash
+# First, convert script (py/sh/R/jl etc) -> notebook. May need additional args to define input format etc as above.
+jupytext --to ipynb script.sh
+# Then, execute notebook in place and allowing cells to produce errors
+jupyter nbconvert --to ipynb --inplace --execute --allow-errors script.ipynb
+# One can also combine these to a single command using jupytext --pipe
+jupytext --to ipynb --pipe-fmt ipynb \
+  --pipe 'jupyter nbconvert --to ipynb --execute --allow-errors --stdin --stdout' \
+  script.sh
+```
+
+In each of the above, `jupyter nbconvert` could be replaced with any alternative tool to execute a jupyter notebook non-interactively, including [papermill](https://github.com/nteract/papermill) which would allow notebook parameterisation.
+
+
 ## Notebook and cell metadata filters
 
 If you want to preserve (or filter out) certain notebook or cell metadata, change the value of either `notebook_metadata_filter` or `cell_metadata_filter` with the `--update-metadata` option. For instance, if you wish to convert an `.ipynb` document to a `.md` file and preserve all the notebook metadata in that document, run