Msconvert automatically cleans up .mgf files with multiple charges.
(cherry picked from commit 5983576)
Myrimatch dumps the config into the log before running.
(cherry picked from commit 63daba9)
Fixing MyriMatch invocation
(cherry picked from commit 185cdc1)
Deleting obsolete comment.
(cherry picked from commit 5c854c8)
Added a switch that can disable semitryptic searches for QuaMeter.
(cherry picked from commit 936bc93)
Trying to fix QuaMeter
PeakPicking fix for QuaMeter
PeakPicking fix for QuaMeter
PeakPicking fix for QuaMeter
Fixing the msconvert cleanup script to correctly remove empty spectra.
Obsolete the cache contents because the conversion is now done differently (changes to cleanup of the .mgf files)
Wrapper.conf gets wrapped as wrapper.conf.sample so we can simply unpack the .tar.gz and not nuke our active config files.
Merge branch 'atlas_dev'

Conflicts:
	lib/mgf/src/main/java/edu/mayo/mprc/io/mgf/MsconvertMgfCleanup.java
	lib/mgf/src/test/java/edu/mayo/mprc/io/mgf/MsconvertMgfCleanupTest.java
	services/msconvert/src/main/java/edu/mayo/mprc/msconvert/MsconvertWorker.java