In progress, Merlin going down so committing.
Commiting because need to switch to another branch.
SetupNavigator has first draft database handling for coarse time
offsets. CalcCoarseTimeOffset plotter copied from PlotTDiff will
do work of calculating offsets for timing algorithms.
Error in grabbing pedestals from SetupNavigator was fixed.
Committing to move to another computer. Added threshold cuts to *NoShift* geenerators and gave them modules argument passing for the threshold value. CFTimeNoShift now accepts the CF arg as well.
MakeAnalysedPulses now drops the '(' out of the arguments it loads, and CFTimeNoShiftAPGenerators looks for arguments named after their number instead of named after their...names
Fixed issue where one couldn't use the TAP with different configuration strings.
Grabbed the right argument in MaxBinNoShiftAPGenerator
TAPGenerators can now take named options. This required making a
new method for TAPGeneratorOptions that grabbed the
TAPGeneratorFactory instead of the modules::options::factory so
that the correct argument list was grabbed.
Added calibration argument to command line parser.
Reformatted command line parser a little to better reflect the
output of the help.
Setup navigator now checks for whether this is a calibration
or not, and therefore whether to freak out or not about missing
tables in the calibration database.
Indentation changes in SetupNavigator code
Merging in calculations into PlotTDiff
Renamed CFTime generator and added a feature to not load time shifts.
Deleteing old files.
Added `IsPairedPulse` to check a TDP has fast and slow pulses
IdChannel throws exception if bad detector name given to... some function.
CFTimeMBAmpAPGen now takes argument to forego shifting the time.
PlotTDiff takes some arguments for the time axis scale.
Merge branch 'feature/toff_rootana' into develop

Conflicts:
	analyzer/rootana/src/plotters/PlotTDiff.cpp
AE: Rename PlotAmplitude to PlotTAPAmplitude
AE: Extend the renaming to the production.cfg file
AE: Rename PlotTime to PlotTAPTime
AE: Rename PlotIntegral to PlotTAPIntegral
AE: Actually rename PlotIntegral to PlotTAPIntegral this time