There is some (very rough) API documentation at...
http://www.cambam.info/doc/api/It still needs a lot of work though.
Much of this is automatically generated so it can be rather sparse on details, but may help to show what classes, properties, methods etc are available.
Regarding
ApplyTransformation():
This does not reset the Transform matrix to identity (no good reason why it doesn't

).
The routine may also fail and return
False. This can happen if the transformation is not allowed for a particular entity. For example trying to stretch a circle will fail (as it will no longer then be a circle),
whereas scaling and translating are allowed as these just change the radius and center point.
So the recommended way of using this method is...
if ent.ApplyTransformation() then
ent.Transform = Matrix4x4F.Identity
end if
In this way, if the transformation is allowed, apply it and reset the transform matrix to identity,
otherwise leave the transform as is.