intermediary commit - started updating readme

README.md

@@ -7,24 +7,59 @@ HeRC Matrix Tools is a collection of open source sparse and symmetric matrix too
 
 HeRC Matrix Tools encompasses a number of tools and libraries to make working with symmetric matrices easier, enumerated below. 
 
-## Matrix Explorer
+# Documentation
+
+Some special purpose documentation is kept in `doc-extra` in markdown format. All other documentation is generated by Doxygen. Doxygen output is not tracked in git, but compiled copies of said documentation are included with project releases. 
+
+Documentation may be built manually with `doxygen Doxyfile` in the TLD of the project. 
+
+**NOTE**: documentation for C components of the project are not listed in the "class browser" - you must use the "Files" tab, then select the file you wish to view documentation for. 
+
+# Current Features
+
+## Python 3.X
+* read/write access to the file formats:
+ * mtx
+ * bxf
+ * valcol
+ * mat
+* conversion of matrix to/from scipy.sparse and numpy dense matrix formats
+
+
+
+# Major Libraries & their Purposes
+
+## Herc Explorer
 Wraps most libraries and functionalities provided by the hercm project within a command line interface. Includes the ability to read and write matrices in a variety of formats, preview or plot matrices, and perform a variety of operations on them. 
 
-## libHercmIO (python)
-Aggregate IO library for hercm python code, wraps code to read and write matrices in all formats support by hercm python code. 
+`src/python33/HercExplorer.py`
+
+## libHercmIO 
+Aggregate IO library for hercm python code, wraps code to read and write matrices in all formats support by hercm python code.
+
+`src/python33/libHercmIO.py`
+
+## bxfio
+C BXF library. Currently supports read only access to BXF matrix files in C.
 
-## libHercmIO (C++98)
-Provides BXF IO for C++, with read-only valcol support planned. 
+`src/c/bxfio.c`
 
-## libBXF 
+## libBXF
 Provides read/write access to bxf format files. 
 
-## libValcol
-Provides read/writ access to valcol format files. 
+`src/python33/libBXF.py`
+
+## libValcolIO
+Provides read/write access to valcol format files. 
+
+`src/python33/libValcolIO.py`
 
 ## libHercMatrix
 Provides a feature rich class type for sparse matrices, and includes scipy/numpy interoperability. 
 
+`src/python33/libHercMatrix.py`
+
 ## matrixUtils
 Provides user-interface centric utilities pertaining to sparse matrices, generally used almost exclusively by MatrixExplorer, but is provided as a separate library to facilitate automation by other scripts and programs. 
 
+`src/python33/MatrixUtils.py`