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alert s/l/c/o indexing

Baltzell, Nathan requested to merge iss272-alert-indexing into development

Created by: baltzell

This should be one way to index consistently within ALERT itself (every exposed index starting from the same "zero"), and with the other detectors (that "zero" being 1 for used indices).

Note, this requires a change to GEMC to remove a manual +1 (only for wire number) in the perl script that converts from COATJAVA geometry to GEMC text files.

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