vpr: Improve commenting of timing graph construction code

Added a large top-level comment walking through how VPR models
netlist/architectural primitives as a timing graph, and the various
transformations used to convert the netlist into the timing graph
(includes several ASCII diagrams).

Also includes discussions about how the code goes about performing those
transformations and some of the additional complications (like clock
generators).

Author: kmurray

vpr/src/base/atom_lookup.cpp

@@ -160,6 +160,6 @@ void AtomLookup::set_atom_pin_tnode(const AtomPinId pin, const tatum::NodeId nod
         atom_pin_tnode_internal_[pin] = node;
     }
 
-    //Each tnode maps to precisely one pin
+    //Each tnode maps to precisely one pin at any point in time
     tnode_atom_pin_[node] = pin;
 }