> On further thought, if done this way, then --update could instead
> serve to update file that already exists, whereas the default would be

I would prefer this, as I might have a config with repo A and B for which
I have changed both locally, but I'd only want to apply the changes to B
to the layers setup, writing a new file will update A, whereas using the
old layers setup will leave A as is.

> to overwrite the file with a new one.

To clarify as it is not entirely clear this is what you suggested.

Use '--update' as a boolean flag which determines whether or not to use
the old layers setup or write a new one
and use an additional '--use-custom-reference repo' option to determine
for with repo to use the custom reference.

This leave the question of what to do if only the '--reference' option is used?
Do nothing or update/use a custom revision for all repos?
An separate option like '--use-custom-reference-all' seems undesirable to me.

Sincerely,

Jermain Horsman
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