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Enable SMOG2 flag in all sequences

Saverio Mariani requested to merge samarian_always_enable_smog2_flag into master

As also mentioned in #518 (closed), withSMOG2 flag is required to be enabled by default for all physics sequences, so that change of TCK is not needed when we decide to inject gas. Reference changes are expected due to the addition of the SMOG2 lines.

As a consequence, some tests from the Allen ci are removed, which also contributed in speeding up the testing sequence.

cc @oboenteg to take it into account when testing downstream cc @cagapopo

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