tools.py: added try/except query for ecaccess-job-list because calling this command sometimes results in an error; waiting helps

Sb: added python script to check for missing files among the flexextract-ed ones. Save the list of missing files in a txt

apl: tools.py - added check for too many active jobs; EcFlexpart.py - added removing of flex_extract files after ectrancs was successful

updated file execution permissions and removed tabs; corrected output of makefile in local application mode

changed cds api retrieval for single levels to retrieve from CS3 disks instead of MARS - severe performance boost

Changes due to Manuscript review for Fortran part (Petra)