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Slight troll, but a valid solution nonetheless: https://twitter.com/KITCTF/status/777628306954944514 

Basically we figured out that the tool uses the same algorithm as https://pokeassistant.com/main/ivcalculator and returns the flag if the Pokemon has 1337 CP and hidden atk/def/stam scores of 13/3/7.
We tracked down the source of its algorithm: https://www.reddit.com/r/pokemongodev/comments/4t7xb4/exact_cp_formula_from_stats_and_cpm_and_an_upd...  Then we extracted the list of Pokemon + base stats that the ivninja tool used and noticed there are some extra Pokemon, one of which (Bininja), has a level/hp combination where 13/3/7 are the only possible hidden IV stats. We needed to do some trickery with the CP level arc in order to make it deduce the correct Pokemon level from the trainer level.