Added trunk folder for main code
Initial check in of the files.
Finished modifying pulsefinder_cluster_sq class file for using the compiled pulsefinder and the sq submission.  It seems to work much more reliably than the Matlab scheduler.  Also modified cluster_sample.m for the new class. Changes to the user are that the submit method now takes a pulsenumber argument and that when adding a pulse a time estimate must be given.
Fixed the spins.nb issue Gina noted.
Added the helper files: smoothpulse and Fvscsandrf.  Also fixed global definition of pulses in pulsefinder_main so that matlab stops complaining.  Now return pulses_out instead of global pulses.
Refixed (version on sharcnet was not in the initial import) the evaluation of the params file so that it works in compiled versions too.
Changed smoothpulse to use interp1 for resampling to simplify the code and generalize it.  Previously it used an aribitrary 50ns resampling.
Test for Gina
Added make_bruker_shape.m to the repository.
Reset pulses structure to empty so old results aren't returned.
No real changes.
Make brukerflag in make_bruker_shape.m a input paramter.  Use nargin so previous usage is not broken.
Tiny i -> 1i change
Cleaned up Fvscsandrf.m to use puslefinder_calcprop.  Also changed calling syntax so that rfrange and Hamiltonian range are now input as arguments rather than hardcoded.  Simulations are now done over a 2D grid and a contour map or 2D plot are returned.
Made the parameters of the onoff ramp penaltyfunction set in the params file rather than hard-coded.
BIG USER CHANGE!  Parmeter files are now functions that return params.  This will allow multiple lines and is more elegant.
Changed the definition of nbspins to work with state to state and unitary search types.  
And changed tstepflag to params.tstepflag.
Edited the sampleparams1 file to be compatible with the updated pulsefinder code by making it a function and adding the onofframps penalty parameters.
Fixed up help for brukerflag.
Added cluster module for Debbies cluster. Forced to switch back to script parameter files.  When calling pulsefinder_main you now must specify extension of parameter file.