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Updated MatrixDevTop (markdown)
related to #5
Add/Update MatrixDevTop.md
Updating regression-test-add to current trunk behavior
Added link to "matrix.py" anchor
Updated the matrix.py -h printout and directory structure
converted to 1.6 markup
Updated the matrix.py -h printout
Added a link to MatrixDevBlueprints
Updated directory structure, matrix.py help, and reworded customizationroot part
Reordered list of links by rough priority for developers.
Removed directories related to old version of MatrixTDB
Added link to MatrixMorphology
Added a bit about matrix.py
Added directory structure and intro prose
Fixed a link, added an example to CUSTOMIZATIONROOT section.
Added subsection about CUSTOMIZATIONROOT