Don't set prototype for prototype contexts included via direct reference
Don't set prototype for prototype contexts included via direct reference

After a SyntaxSet is built once, all the references are replaced by
direct references (via index).

When it's converted back to a builder and then built again, the code
that marks prototypes needs to handle those references too, otherwise
some contexts include the prototype when they should not.

Fixes #219.

trishume/syntect