> mkdir test
> cd test
> git init .
> mkdir ba
> mkdir ba/ca
> 
> # So far so good.
> # Should clean directory "ba/ca"
> git clean -dn -- ba/ca
> 
> # Should clean "ba/ca" and ignore non-existent "j"
> # Instead, it wants to delete "ba" totally.
> git clean -dn -- ba/ca j

actually, my git will also do it wrong when 'j' exist, do
these after your script:

$ git clean -dn ba/ca j
Would remove ba/
$ mkdir j
$ git clean -dn ba/ca j
Would remove ba/ #here missing 'ca'
Would remove j/

I think it's the problem of directory path manipulation.

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