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Updates in analysis for producing graphs etc. for CTE2015 website, plus some minor changes for Eric's SAM runs.

Added additional options for South America fwd runs, including option to run forward when no observation is found in that cycle.

(1) Start up assuming that the statevector and CycleControl still need to be setup. This allows
stand-alone operation of this pipeline

(2) The analysis pipeline no longer needs the obsoperator object

(3) The pipeline crashes on errors, there is no try/except anymore for each part

modifications to archive pipeline to allow multiple rsyncs with custom selection of folders to sync, see template.rc for example

Added option to transition from 25 to 34 layers for OD meteo after December 2005. Added option to read initial random seed from file. Localization method is now read in from rc file. Changed terminology of mixing ratio to mole fraction.

rename *PlatForm to *Platform

renamed class names Ct- to CO2-
changed class name Observation to Observations 
small cleanup changes to template.py

in sv.write_to_file modified the prior/optimized identifier in function call to be prior/opt text instead of True/False

changed the function calls in order to remove need of sth.DaCycle = DaCycle in start_job. achieved by adding DaCycle to particular function calls and initializing tm5 with DaCycle as call parameter

added the get_covariance generic function to the sv baseclass

write_members_to_file: is called with _lag_ instead of lag +1, as inside there was a "lag-1" call... that one removed from inside as well

write_sample_info changed to take the whole path as a parameter: so now we explicitly see the path in pipeline, plus we don't need to return it back.
same for write_obs_to_file

managed imports in obs files

removed a need of using samples.DaCycle=DaCycle (now it is only passed in the "initialize" function)

removed StateVector.isOptimized and replaced with an "optimized" parameter in StateVector.write_to_file call

in obs and obspack_geocarbon adding some parameters to function calls

removed "oldstyle" and "newstyle" checkings from write_obs_to_file (it was added for debugging purposes at some point...)

Changed R and HPHR matrices to vectors for serial minimum least squares algorithm in optimizer to save memory (the routines needed only vectors). For the bulk algorithm this is not possible, so nothing was changed for that option.

Changed the localization routine and settings, so that the localization is actually used. Also added some extra logging messages related to localization.

Minor changes to flow of sample_step and sample_state. Caught a possible problem with the get_initialdata for the ObsOperator, which also needs to happen for an advance step.

Implemented the first outlines of a ForwardPipeline that simply runs TM5 with optimized parameters from another run. To be completed...

reverted to r1186 (the last one from 2012), with changes in observation files from r1192-1194 preserved

called from pipeline as call parameters
*warning* take care about get_covariance, it is called from baseclass's "propagate", whereas this function exists only in the derived class.