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

Changes for South America runs: regions files in analysis directory are copied from the one specified in the system.rc file. Region pickle files are deleted in the analysis directory, to make sure the correct one is used. Option to use covariances for less than 23 transcom regions, but still use 23 for the analysis (does not work in tcfluxes.nc). Update in observation_operator.py to use restart file in first cycle also for more than one resolution (i.e. incl. zoom regions).

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

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)

a lot of my helper comments, but they will disappear soon.

performed actions discussed in email #2
removed unused __str__ functions
a bit of ordering of the pipeline.py

ct/tools.py (whole file)
tm5/observationoperator.py: WriteRunRc
tools/initexit.py: SubmitSubStep
tools/general.py: CreateLinks, ToDectime, StoreData, RestoreData

- reduced to one the two-command messages logging 
- removed unnecessary commas and brackets in tuples definition
- removed unused imports
- __str__ definition: changed print to return
- removed unused values attribution ("dummy = ...")
- formatted the code
- repaired bad indentation
- removed dummy returns ("return None")
- removed non-meaning body of baseclasses.optimizer.Localize()