It is strongly suggested not to modify code outside of the cp interface.
Due to some info is placed in the database from the cp and unless you know exactly what you are doing you could hose your board.
For example styles even though there is a text file for each style it is stored in the database and they must match
But here it is.
under the Includes folder.
config.inc.php config file that holds some of the values plus body onload
header.php
footer.php
header-insert.php
