I would be interested in trying Agile Toolkit however I hate the CSS framework it uses and also the html markup.. is there any means to use a custom CSS framework like jeet and also to change the html cluttered markup..
Can you hack away at the source files with this framework or is that not advisable ?
It seems good however I am wondering if it is the sort of thing a beginner would use as it provides UI elements etc that are pretty basic and assume no understanding of design or frontend programming
I'm currently working on the next iteration of Agile UI framework, which will migrate away from the Agile CSS and will use "Semantic UI" (and perhaps also Bootstrap as alternative).
You are welcome to try it out as I'm developing:
http://github.com/atk4/ui
To answer the rest of the question - the "HTML/CSS" is interchangeable and the core framework tries not to rely on any specific "classes" or "patterns" that CSS framework uses.
I know that ATK 4.3 has port to Bootstrap and Semantic UI somewhere in here: https://github.com/xepan/.
Concept of ATK should be both usable by beginners or are more experienced developers that strive to build web application that are less specific about implementation details and instead look for more consistent and faster-to-create user interface.