start of parallel make improvements
updated branch version header file from v2.4.1 to v2.5.0
added bam2starchcluster script
updated Makefile to install bam2starchcluster with conversion scripts
Update bam2starchcluster.tcsh

Updated the usage statement to note script name
add --wmean1 operator to bedmap; 1 variant of the weighted mean
made chromosome name lookup process more generic in bam2starchcluster script
updating Sphinx (readthedocs) configuration file to test math markup module support
updated README version numbering
updated documentation version numbering and clarified details with conversion scripts
testing math markup ReST file
modified third-party library targets to build under OS X
updating makes for parallel compilations
recovered alex's upgrade to jansson 2.6
updated maek
Updated version number in OS X package project 

Changed from 2.4.2 to 2.5.0
fixed linux make break
fixed linux builds
set up foundation for duplicate and nested element flags in starch v2->v2.1 spec upgrade
changed permissions: bam2starchcluster