Removed unnecessary .gitignore from subdirectory
Removed obsolete manual-changes.txt file
Changed Soar manual generation script to use moin2latex like old version instead of html2latex. Now pulls from soar-cli-documentation repository instead of wiki.  Files there use the same markup as we were using on google code.
Added changes neccecessary for a new SVS chapter.  Manual now compiles for new git repo with proper table of contents.  Currently just points to an empty placeholder chapter, but