Refs #6550 Added options for finer control

Refs #6591  Changed the name of IndexOptimizePeaks to OptimizeCrystalPlacement
Refs #6142 Eliminated(hopefully) several warnings or explained them.
Refs #6550 Added properties to OptimizeCrystalPlacement

-Properties to select the peaks used in fitting were added.
-A boolean property was added to select whether sample offsets are to be
  considered in fitting
-Changed the names of several properties and gave longer prompts
-Eliminated IndexPeaks optionq
-Sped up the test program  a lot. The LoadIsawPeaks now takes almost all the time.

Refs #6086 Added Documentation and explanations