This routine now also opens the optimizer.nc file and retrieves the forecast values. Then these are written to
the observation files too for later use.

Note that with the current processing chain, it is expected that the format of observations is ObsPack!

This routine can be used to plot time series and histograms of mole fraction data. It can be used inside a CTDAS job to produce these figs after each step,
or it can be used stand-alone by modifying the last few lines wehere a DaCycle object is created.

A new routine has been added that summarizes the X2 statistics for all time steps, and for all sites. The result is an html table in the analysis/summary folder.

This new analysis script writes a summary of the observations that were sampled to a html file. Note that it currently only works with an ObsPack observation object,
because of the file structure assumed on the input side.

An extra LoadRc is needed in Initialize() because the tm5.rc file we want to use is not necessarily the one that was specified on the command line when starting the cycle. This is the case in a recovery from a crash for instance, where we first replace the da_runtime.rc settings, and then we also need to tell the system that we are using a new tm5.rc file (the one in the run-directory, and not the one on the command line).

The code now compiles itself on a clean start, and then proceeds with the rest of CTDAS. The name of the tm5 rcfile is modified
to reflect the new name and location (something like ${rundir}/tm5-tm5-ctdas-base.x). This file will be read, modified, and rewritten
in each sample step of CTDAS. This file already contains a proper submit.command key which can be used to submit TM5 runs automatically, he script then handles the details of the queue system etcetera.

To Do:

- modify the Run() routines to use submit_tm5 (Ivar)
- modify the PrepareRun() routine to make sure all needed keys are replaced in the tm5.rc file
    - such as the submit.option : -s !!!
- test for multiple cycles
- test with a restart option to check logic of compiling