Back to 2J=sqrt(2J)^2, and Calculation fixed

For the purposes of testing the code, we have returned to the old way of
calculating 2J, but all the new calculations are kept and can be
implented.  There was a bug in finding the commonbpms in gen_kick_calc()
but this has been fixed due to new helper function in utilities.
Merge branch 'master' of https://github.com/pylhc/Beta-Beat.src
Commit to fix bad indentation
Merge branch 'master' of https://github.com/pylhc/Beta-Beat.src
Added new testdata for drive test
Changed double compare value and set test flags to run all tests

Changed the relative value for comparing doubles to 1e-4.
Changed flags so that the exhaustive drive test will run.
Fixed a bugs in SegmentBySegment.py

See github issue #38
Changed delta_phase to avoid program crashing.
Fixed looking for getphasey_free.out file.
Replaced excepts with except (IOError, ValueError)
Possibly corrected changes

Added also a todo for Andy.
Inserted ProgramVersions.properties again

I deleted this file instead of FFTTerms.txt.
Deleted also FFTTerms.txt
Merge branch 'master' of git://github.com/pylhc/Beta-Beat.src
Correct position of initial comments
Merge branch 'master' of https://github.com/pylhc/Beta-Beat.src
Fixed getphases calls and refactored getcoupling

Fixes #23 Inserted for tune values None and get_phases checks if tune_q
is not none before fixing shift in LHC
Refactored coupling a little bit. Changed names and extracted duplicated
code.
A start to organizing drive

The main function in drive is too big.  A few functions have been added to
begin compartmentalization.
init ndiff.py

Created python wrapper for python. Renamed and moved numdiff binaries.
Added README and default configuration files.
Merge branch 'master' of https://github.com/pylhc/Beta-Beat.src
Adapted filecheck of GetLLM to use ndiff for comparing
Changed path to binaries in CTestSetup.cmake and cfg file ends with a
newline
Added function to compare dirs in ndiff.py

Adapted drive test to use ndiff.