There are several important files in the hacksuite you should know about if you want to code tools for the hacksuite. I'll try to sum up most of them and explain their features and why you need to know about them.

root
vars.php: sets important context variables and it's default values
header.php: loads all the important variables and settings that the hacksuite needs in order to function properly
paths.php: sets paths dynamically, these are simply shortcuts to folders and some files. It's essential to remember them and never use absolute directory paths.
default.php: this is the index page of the hacksuite, you can easily customize the output as long as you keep in mind that the output is in variable $sCode

data
Data/extra.php: contains an array with paths and names of the installed apps
Data/reserved.php: reserved folder names
Data/running.txt: holding the tasks that are running and are already completed, you can use the task manager in the configuration to manage them
Data/version.php: contains the current version of the hacksuite

includes
Includes/log_error.php: logs errors depending on your configuration
Includes/render_headers.php: renders the headers for the html page
Includes/screen_header.php: this file required to load the into the iframes aka screens in modules or your own apps
Includes/server_setup.php: sets up the testservers
Includes/task_end.php: doesn't really end the process, instead it ends the task in the task file
Includes/task_start.php: starts the task and creates an entry into the task file
Includes/wordlists.php: used to create a form where you can pick a wordlist to use in an attack or whatever you want to use it for

logs
Logs/login_single_user.php: this file is used by the test server to simulate login failure logging
Logs/thc.txt:
this is the default log file where all errors will be written to

templates
Templates/x/index.php: this is the template that will be used to create all pages in the hacksuite

test servers
TestServers/login_single_user.php: html login server that you can use to test your scripts against
TestServers/http_authenticate.php: this is the http authentication server

wordlists
Wordlists/pw_a.txt: the one and only wordlist for the hacksuite, well you can just download some more and add them to the Wordlist folder.