I don't think Boonex is using any standardized format and each individual developer is implementing their own "standard" when they work on the code. I think some of the bugs clearly show this when the issue involves css. I put a Spy.css bug into TRAC, told them where to find the problem and how to correct it, and the thing has sat there for weeks even when a dev picked it up (still there as of today). They have to hunt through the code the same as us to find the issues.
If we had see more a concise program tree, development and standardization could really start but I don't think they even have that. To best standardize the program would be to place it into an existing framework (Zend perhaps) which would force standardization and make modifications/error hunting soooo much easier. I know this will not happen for D7 but lets hope for D8 that they do use a framework. Using the framework will provide simple standardization and professional urls. I hate how we have site.com/join.php where if we had a framework it would be site.com/join and the user would never see the *.php extension. Something to think about.
If we had see more