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According to Detective Conan World's Wiki, there are a few people who know Conan's real identity. I checked out the list and found Hajime Kindaichi.

I am a fan of Kindaichi series so I would like to know how did Kindaichi get to know Conan's real identity? Obviously Conan wouldn't have told Kindaichi himself. Kindaichi must have figured it out.

So is there any special episode or a manga chapter where Conan and Kindaichi work together?

I know about the game.

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As of current writing, there's no special episode/manga chapter featuring the crossover of Detective Conan and Kindaichi Case Files.

The only real crossover is the Nintendo 3DS game (as you already mentioned), called "Meitantei Conan & Kindaichi Shounen no Jikenbo: Meguriau Futari no Meitantei" (or "Detective Conan and The Young Kindaichi Files: The Chance Meeting of the Two Great Detectives").

Other than the game, there's a collaboration between Weekly Shōnen Sunday (Detective Conan) and Weekly Shōnen Magazine (Kindaichi Case Files) to celebrate 50th anniversary of Sunday Magazine by publishing a twelve biweekly magazines consisting of chapters from both series (full list of the chapters can be read here (in Japanese)). It's only a collection of chapters from both series, not a crossover though.

Other than that, there are canned coffee featuring both characters, and a Game of Life featuring both series.

Reference:

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