You can find all of the api here:
core\xpdo\om\modx095\modx.class.php
and the parser is loacated in
core\xpdo\om\modx095\modparser.class.php
with an extension for backwards compatibility in
core\xpdo\om\modx095\modparser095.class.php
That really is the main directory that makes everything work, there are also files in there for caching, session handling, and db. The mysql folder that is inside of that, contains all of the object mappings to the database and the classes to access the database objects.
Hope that helps, Jason should be able to expand more on all of this if needed.
p.s. Jason, let me know if I spoke incorrectly on anything