better wrap permutation operations into the STk interface

Graph.h: reconcile methods and functions accepting Graph* and Graph&

fix manual generating program so it doesn't generate index entries with
names starting with "Prog" or "User" - probably eliminate the use of 
c_filter.cc - just use filter for both .tbl and .crt

change method definition to test whether symbol defined, define it if not
(instead of defining it in C++pointer.cc)  will make startup even slower,
but extending easier.

fix leak in dissolveSubgraph - some memory is not deleted that should be

include option to output Polka animations 

incorporate protocol like Tcl_Dynamic, etc. for dealing with dynamically
allocated Attributes (currently leaks them)

Manual:  ProgDFSTest.cc doesn't compile because List<AnimationData*>
         isn't instantiated and some STk stuff makes it in (run make libs?)

segfault: (define g2 (graph '(1 2) '((1 2) (2 3))))

Linux distribution should have individual template instantiations and no
libraries.

parser:  keywords "GRAPH UBINGRAPH" (etc.) should not be mandatory, but
         they are currently needed during parsing of graphs with subgraphs.

vertex-size: changes in *link:default-vertex-size* should cause a change 
	     in C++ default vertex size.  Currently DEFAULT_VERTEX_SIZE
	     is a symbolic constant.
