How to move all theme templates into a subfolder WP

Not easy to do. You can create redirect template and assign templates based on page ID 

    <?php
    if (is_page('629')) { include(TEMPLATEPATH . '/pages/homepage.php');}
    elseif (is_page('186')) { include(TEMPLATEPATH . '/pages/generalpage.php');}
    else { include(TEMPLATEPATH . '/pages/defaultpage.php');
} ?>

See this for more details

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