Q:

HashMap.this.clear() what does this mean, how does this work

In HashMap class there is an inner class KeySet whose instance is returned by the HashMap's instance method keySet().  This inner class contains the following method. 
public void clear() {
    HashMap.this.clear();
}

I understand the general semantics of "this"

It is a reference to the "current" object.  
Can be used within constructors or any instance methods where it acts as a reference to the object being constructed or the object whose methods are being invoked. 

The above style of using "this" seems interesting, 

It is being used as if its a static variable of a class.  
It should still be referring to an object whose method is being invoked.  In this logically it should be an HashMap instance. 

Given the above two it should be possible to have a static reference to any dynamically created instance object but that's not possible since there could be infinite number of instances at runtime and there aren’t any language constructs to specify this relation between a class and its instances. 
I am definitely missing something, can someone help me understand this better.  

A:

When a non-static inner class is created, it gets a reference to its enclosing class instance.  In order to reference that instance, a special syntax is used: the keyword this is prefixed with the name of the enclosing class.  When used without a class name prefix, this keyword refers to the instance of the inner class itself. 
Essentially, the call is made to the clear method of the HashMap class.  Note that since the method of the inner class is called clear as well, the call without HashMap.this would have been directed to the clear() inside the inner class, causing infinite recursion. 
As correctly stated by Roger Lindsjö in a comment below  Technically the idiom is known as qualified this construct. ( JLS 15.8.4)

A:

HashMap.this.clear(); calls the current instance of HashMap, you mentioned that its calling from a InnerClass, so that's how its referencing the Outter class.