Fixed: Formula::Flatten() handled positive literals like definitions.

Formula::Flatten() manages a term-to-var map to avoid unnecessarily
new variables. The map is initialized with all variables that are 'set'
in the clause already. That is, every literal (f(...) != x) boils down
to an entry that maps f(...) to x.
The bug was that this entry was also made for (f(...) == x) literals.