Fix count function deprecation warning

[PanderMusubi]

PLease fix this deprecation warning:

./duplicate_finder.py:175: DeprecationWarning: count is deprecated. Use estimated_document_count or count_documents instead. Please note that $where must be replaced by $expr, $near must be replaced by $geoWithin with $center, and $nearSphere must be replaced by $geoWithin with $centerSphere
  return db.count({"_id": file}) > 0