Hello there!
Although Cotonti doesn't have the biggest community, and support is rather limited; Those who do help know what they are doing. With that said, I believe you have made a great decision by choosing Cotonti for your website. Now to answer your questions:
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Every theme consists of those TPL files you mentioned (for each individual page). In addition there are a few PHP files associated to every theme as well.
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theme_name.en.lang.php - This file(s) allows your site to be multi-lingual by having individual language packs. Cotonti by default comes with core language packs, but each theme will need their own as well. Note the "en" part is interchangable with each language abreviation (i.e. en=english, ru=russion). If you open the english language pack you will see something similar to this:
$L['Contact'] = 'Contact';
Now in your TPL files that value can be called by using this tag:
{PHP.L.Contact}
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theme_name.php - This file defines your themes name, and the schemes associated with it. It is done so through this portion of the file:
/* ====================
[BEGIN_COT_THEME]
Name=Nemesis ver. 1.00
Schemes=default:Default
[END_COT_THEME]
==================== */
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theme_name.rc.php - I believe it's in footer.tpl now, but there is a tag {FOOTER_RC}, which contains these javascript/css files that you want includes.
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I know we used to have a complete tag list, but unfortunatly I don't remember where it is located. I'm sure someone will reply to this thread with a direct link though (if it still exists).
If you have any more questions please feel free to ask, i'd be glad to help you out!
We are what we repeatedly do. Excellence then, is not an act, but a habit.