ignore pom backup

Use CeCILL-B (BSD like)

The atom mapping being performed in parallel, splitting resources between simultabeous aam tasks seems to be sub-optimal. To investigate further

fix bug with transport reactions

fix system exit caused by reaction O=C(O)C(NC(=O)C1N(C(=O)C(N)CC=2C=CC=CC2)CCC1)CCCNC(N)=[NH2].O.O>>O=C(O)C(N)CCCNC(=N)N.O=C(O)C(N)CC=1C=CC=CC1.O=C(O)C1NCCC1

create fat jar with dependencies during build

switch back to sequential for now, doesn't seems to affect perf much

remove duplicated lines + easier to parse (cpd or rxn ids extraction)

provide a filewritter to the logger. Logs are duplicated

the "keep" function was doing redundant computation if reaction already checked for flaging. The keep method now only look for no-go flags and a quick one allows to avoid full check