Moved the writing out of the "0" to the fDumpOut for hodo calibrations
to immediatiately after the TOF with track info calculations.
Before it had been after then lines

  if ( !fChern || !fShower ) {
    return 0;
  }

so if Cerenkov and shower were not used in replay the code would not get
to write out the "0" which is used to denote the end of an event data for
the calibration script.

PSE125 holds information about setting of F250 modules. Now this
information is used to set `fNPedestalSamples` and `fNPeakSamples`
parameters of `THcRawAdcHit`.

This is done through `THcHitList`, since it has information about
which crate and module each channel is in. Currently, the information
is set for each event, because of the hitlist and analyzer design.

I added the neccessary support for these changes to all raw hit
classes.

  Provides methods get NSA, NSB, and NPED for each crate

Corrected warning message for missing refchan to correctly display reference channel.
Modified warningg message for missing refindex to include information about reference channel.

	Cycle over array of pedestal subtracted fADC signals fA_p in
	the same order as it was filled.

fScinHitPaddle is a std::vector<std::vector<Double_t>>. It was
cleared and rebuilt for each event with the same structure,
instead of just zeroing out all the values.

Now it is created in only one place, and than zeroed instead of
cleared.

Changed data type in fScinHitPaddle from Double_t to Int_t. Should
be changed to bool, but then all logic should be changed.

There was a weird bug in the code, that only triggered for some runs.
It turns out, in the `THcHodoscope::FineProcess` the hits in each plane
were created only for number of paddles in first plane. SHMS, however,
has 13 paddles in first plane and 14 and 21 paddles in last two planes.

The problem is fixed now, but part of that code should be rewritten for
efficiency.

With the new raw and good varibles added to the tree, these variables are not needed in the tree.

Applied changes in several files to reflect this.
Minor fix in `THcRawHodoHit`.

When calculating the residuals, consider all track candidates instead of only the first track.  Moreover, eliminate the instances when there was no hit in a plane then the residual was returned as zero.

This error is triggered when there is no wire defined for hit, or
when the wire has no `GetTDDConv()` method. The ROOT dictionary
calls default constructor that doesn't set the wire and calls
`ConvertTimeToDist()` regardless.

I changed the default constructor to not call the `ConvertTimeToDist()`
if the wire is not set. I also added the call to this function
in the `SetWire()` method.

The fCosmicFlag is used in EstimateFocalPlaneTime
The start time for the drift chamber is determined as an average
of the focal plane times for each hodo plane. Need to account for
the TOF from the hodoscope to the focal plane (z=0). For cosmic
data need to add this TOF to the corrected scintillator time, while
usually one needs to subtract this TOF. Add a flag as parameter to
switch between these modes.

`THcTrigRawHit` now uses raw ADC and TDC classes.
Added new leaves to the `THcTrigDet` Root output.

  THcScalerEvtHandler will work for rocs with scaler data with or
  without the data being wrapped in a bank.

  This should really be configurable as sometimes there will be
  two Cerenkovs and we should be able to choose which Cherekov the
  hodoscope should use in efficiency calculations.

The calls to `Find()` need to be wrapped in checks if returned pointer is null.
Otherwise a further call to get value produces SegFault. The `LoadParmValues()`
does not suffer from this, since it throws error if non-optional parameter is
not found. The error message also tells which parameter is missing.

I still left three calls to `Find()` in `THcAnalyzer.cxx`. They are wrapped in
checks and some other things...

- renamed internal variables to more vocal names
- added boundary checks to new Get methods
- removed obsolete get methods
- added new get methods
- updated documentation accordingly

Modify default tdc_neg and tdc_pos = -999
SetCorrectedTimes when only oneside has TDC within in window

Added documentation for THcRawAdcHit.

Added channel to time coefficients to the Adc and Tdc raw hit classes.

 - corrected the number of samples used for peak integral to 9.
   This number will eventually have to be read from prestart event.
 - added explicit casts from Int_t to Double_t in several methods

 - Added new leafs to the hodoscope tree.
 - Added new leafs to the aerogel tree.
 - Added new leafs to cerenkov tree.
 - Added new leafs to the shower tree.

Left all the old leafs in there. Will need a careful cleanup...

This makes the code nicer and with less duplication in logic.

Along with that I had to correct all the call sites to the RawHodoHit in all the
classes that use it.

Added new class THcRawTdcHit.
RawShowerHit update.

The f250 modules can produce at most 511 samples (9 bit) so it seemed reasonable to increase
the maximum number of samples in the raw hits to this value.

As it turns out, this was not so easy fix. I had to do:
- add at least c++0x support to scons (works for g++ 4.4.7!)
- change how my DefineVariables works

The c++0x support is bonus, since now we can use some additional features, like auto keyword (see https://gcc.gnu.org/gcc-4.4/cxx0x_status.html).

The new class THcRawAdcHit is meant to represent the raw ADC hits. The
logic with dealing with ADCs has become quite complex now and it would
have to be multiplicated across all detectors that have ADC
channels. While this by itself is not such a big problem, fixing
possible bugs in multiple places is.

I also redesigned the THcRawShowerHit class to use the new
THcRawAdcHit. The redesign was due anyway, so I took the opportunity.

I also had to modify THcShowerArray and THcShowerPlane. They still
need some work to use the the new flash 250 data, but changes were
necessary anyway.

Minor fix 01.

- Now throwing an error for invalid signal in THcRawHodoHit::GetRawData and THcRawHodoHit::GetData.
- THcRawHodoHit::GetData now only subtracts reference time for TDC channels.
- THcRawHodoHit::SetReference now prints warning when trying to set reference time for ADC and does not set it.
- Fix in THcTrigRawHit::Clear to set fHasMulti to kFALSE.
- THcTrigRawHit::SetReference now prints warning when trying to set reference time for ADC and does not set it.