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

flagging scheme now assumes 99 as default (do-not-assimilate) until changed by sites-weights.rc logic