Does a manga like this exist, where the protagonist is a male, and his close friend is a female, but because of her boyish attitude and the way she dresses he thinks shes a male, and doesn't find out the truth till half way through the manga, after which he starts developing feelings for her (or already had them but denied them because he didn't want to be gay, or didn't think his friend would accept his feelings (thinking that he(she) would feel disgusted), but then when he find out that he is actually a girl he gets incredibly happy)?

Not exatcly but Tomo-chan wa Onnanoko!

That's the basic plot of Boku wa Ohime-sama ni Narenai

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My current top 3:
Fullmetal Alchemist
Pandora Hearts
3-gatsu no Lion

I second this. That was my first immediate thought.

Boku girl, gender bend but it's kinda what you're looking for.