[Fix] Improve atom polarity detection in composites inverted index

[Fix] Improve atom polarity detection in composites inverted index

Count NOT operations from atom to root instead of just checking direct
parent. This correctly handles nested negations like !(A & B) where
atoms A and B are both under negation even though their direct parent
is AND, not NOT.

- Even number of NOTs = positive atom (must be true)
- Odd number of NOTs = negative atom (must be false)