Mussagl Manual: Updates for Docs 1.0

Mussagl Manual: Updates for Docs 1.0
 * Moved UCSC tutorial toward end, but linked to from Obtaining Data section.
 * Added animated gif under dynamic threshold section.
 * Documented command line options. (tickets: #167, #225)
 * Mentioned Python existing in Mussagl. (tickets: #167, #227)
 * Updated repeats documentation. (tickets: #167)
 * Updated .mupa file format description.
 * Added note about .mupa comment character.
 * Added a create .mupa section for UCSC tutorial. (ticket:164)
 * Linked to Diane's OverlappingWindow wiki page (ticket:137)