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add deprecation
Removed (outdated) label from Executables
Updated Home (markdown)
Added mention of matlab as an optional dependency
Added direct links to the Configuration File and Command-Line Option sections of the UI page
Added link to the proto-quick-start guide
Fixed the minimum cmake version (2.8)
Updated Katydid (markdown)
Changed the description of Katydid from an analysis "package" to an analysis "toolkit"