Removed old config files from the installation, and updated a couple example config files.
A couple more fixes in the basic example config files.
Removed the Doxygen site from the distribution since it's now hosted on github.
Updated Monarch to current master branch.
Adapted a bunch of classes and executables to deal with the updated Monarch.
Updated PackageBuilder to deal with having a parent build (not that Katydid does)
Removed MonarchPP files.
Fixed some typos
Added KTEggWriter.
Added KTDCOffsetGenerator.
Improvements to KTEggWriter. Plus changed the name of ParsePair to ParsePairUInt, and added ParsePairUIntDouble.
Updated monarch version
Force use of separate interface in monarch-based reading
Update TS generator for new Monarch
Some updates to the EggWriter (still not working). 
Bug fix in KTDCOffsetGenerator.
Updated Monarch again. Minor fixes to CMakeLists.txt and AUTHORS.
Set missing slice header data in KTTSGenerator.
Working version of KTEggWriter, including application of slice header information.