Things get even more interesting when adding

print r.path()

which is different from the other two in SageNB.

For cells and clouds, perhaps the issue is in forking from already started 
processes? Although my impression was that all pexpect interfaces are 
closed in this case and will be recreated only when needed, so if the new 
fork is pointed to a different directory, newly created interfaces in it 
should pick up this directory...

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