Mention the run number when we throw an uncalibrated run
Add global option to dump the input file's content
Make sure we test whether or not to dump the input files
Comment out unnecessary check for channel names to be unique
Add IsGood and CouldBePaired methods to TDetectorPulse

CouldBePaired tells you whether the generator was able to pair pulses in
principle.
IsGood tells you if the pulse should be used for subsequent analysis,
since it was either a a paired pulse (IsPairedPulse) or the generator
didn't actually pair pulses (!CouldBePaired)
Only add good TDPs to the TME and added GetSourceIndex method to help
looping over all sources for a given channel
Big rewrite of logic to select TDPs within TME window.

Fixes #238
Histogram the time difference of pulses w.r.t. the central muon in a TME
Add module to plot the self correlation of a channel with certain cuts
Added a new module to investigate muons stopping in the silicon target
Rename exception to avoid name conflict from SetupNavigator
Move exception declarations into header so other classes can catch them
Added methods to get index of first and last SourceID to match a Channel
ID in a TME (for using multiple sources on the same channel)
Protect against normally pairable channels being missing from a run
Add extra plots to PlotTME_muStops module
Change the default value for the MuSc threshold in the PCF
Swap fast and slow parent channels in the enums so it's the same as the
IDs::channel
Many changes: Style, new plots, better cuts => See muon capture spectrum
Renamed PlotTME_muStops to PlotTME_activeSiRmuStops
replace PlotTME_muStops w/ PlotTME_activeSiRmuStops in code