If by rebuilds you mean the forced reinstallation of a package version 
that's already installed, I don't see what the problem is. The procedure I 
outlined will do nothing in that case. Nothing will be pulled, so no new 
heads will be created. `hg update -c` may fail but I don't see how that's 
inconvenient. If it doesn't fail it will simply update to the head, which is 
hardly an inconveniece. Or am I missing something?

I guess by "where" you mean where the file containing the message about what 
cleanup needs to be done manually after an upgrade should go. I just meant 
that each spkg should append something to, say, $SAGE_ROOT/final_messages , 
and then sage-upgrade itself should cat and delete that file at the end of 
the whole process.

-Keshav

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