same behaviour as old compare-structures

Before the program wrote the traceback into the output json but
exited silently. Now we re-raise upon writing the output.

commited for further review, currently co-exists with compare-structures

Only the fast residue number alignment has the requirement of no insertion
codes and strictly increasing residue numbers.

That was 1) strictly increasing (no idea why it was there in a first place)
2) no ins codes (The residue mapper is a dict which now has actual residue
numbers as key - can handle insertion codes)

RepResult was fixed to not throw errors any more

Conflicts:
	modules/mol/base/doc/entity.rst

The code would previously only consider the last chain mapping in
consideration. As a result we find better scores in tests.

fnat, lrmsd, irmsd etc. are not strictly DockQ related, they just
serve as input for DockQ

Raise a ValueError upon initialization.