"therefore you can have multiple applicaiton classes" - i think will be better "therefore you can have multiple applicaiton classes for one project"
"don’t go outside of your application" - not clear. How can I go outside of my app? If it is possible we need something like "bad example", otherwise i can "go outside" accidentally and do not even know that i did it.
"it will initialize several sub-components which call Controllers" - not clear. Maybe lists of sub-components for each type of App will be good to have here?
It is good to have example of Frontend.php file with db connection, jQueryUI and so on after "it will initialize several sub..." paragraph.
"ApiFrontend will automatically initialize Logger() which makes error logging more bearable." - is any information how to use this logger?
"Layouts A Layout is a region in the shared template". Typo?
"Layouts A Layout is a region in the shared template (shared.html), which is parsed by the API class. If the region is defined, then a corresponding layout function is called." - i think this part can be extended. Don't know how yet.
"most significant layout element is “Content”" - why layout, not template? And why element, not spot? Content is required spot in template.
http://book.agiletoolkit.org/agiletoolkit-overview/application.html