Remove index.php from "Homepage" URL

[agent47]

So I tried making changes to QueryString.php to remove index.php from the URL for SEO purposes and this is basically what I did.

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$scripturl = $boardurl . '/index.php';

Replaced with:

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$scripturl = $boardurl . '/';

but that had an effect on topics as it seemed to break them everytime I clicked on a thread. Is there another this can be done?
I just want my homepage to be http://www.superheroalliance.net and NOT http://www.superheroalliance.net/index.php
That's about it. If it's contained in the link of topics I don't care. I just want my "homepage/main page" URL to NOT contain index.php.

[IchBin]

Removing index.php from the URL has no effect on SEO just so you know. Search engines these days are smart enough to figure things out. There was a mod I think that did exactly what you did IIRC. If you need help with this I'd suggest posting at SMF since it seems to be an SMF problem and not a TP one.