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I wanna to pretty much customize question2answer source code.That's why i wanna to know that where is most of the html code exists to change something on main page.

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The HTML is generated by PHP code. If you want to modify Q2A you should look into creating plugins. You still need to know PHP for that, though.

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Ah...I think, you can find most of the HTML in the qa-theme-base.php file in the qa-includes directory.In fact, there are also many PHP codes that generates dynamic HTMLs.So at first, you should have a primary knowledge of PHP in order to modify html output of Q2A.
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