SliceMonitor and ParticleMonitor now add simulation parameter dictionary to hdf5 files.
Removed simulation scripts.
Created RFQ branch.
Removed simulation scripts.
Merge branch 'rfq' of https://github.com/like2000/PyHEADTAIL into rfq
Merge branch 'kli' of https://github.com/like2000/PyHEADTAIL into kli
Merge branch 'kli' into rfq
Adapted Monitors and Wakefields to comply with the concept of Slices decoupled from Bunch. Ready for testing.
Removed *.html files.
Removed symbolic links and #..# files.
Re-added *.pyx files. Removed *.c.
Renewed *.pyx files.
Changed scope of variable 'wake_field_keys' in 'wake_fields.py'.
Fixed bug in ParticleMonitor. 'yp' was mapped to 'xp'.
Fixed index bug (i:i+1 -> i+1:i+2) in _set_slice_index_of_particle().
Slight modification of 'Wake_table' class in 'wake_fields.py'.
Modified 'transverse_tracker.py' to correctly segment 1-turn integrated
quantities (like eg. app_x,y or Qp_x,y). General cleaning.
Fixes bug in _set_slice_index_of_particle() when using 'const_charge'.

'const_charge' and 'const_space' use different indexing
conventions for first_index_in_bin -> Use z_index attribute
instead for slice_index_of_particle.
Extends 'transverse_tracker.py'.

- Adds support for octupole cross terms app_xy, app_yx.
- In 'detune' method:
    - Adds effect of octupole cross terms app_xy, app_yx.
    - Makes implicit dependence of octupole parameters on p0 explicit.
    - Adapts definition of Jx, Jy.
- Adds convenience function to get octupole parameters for LHC from magnet
currents.
Added 'close' functions to monitors to savely close hdf5 files.