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Add file output to I/O thread

Daniel Charles Craik requested to merge dcraik-writeOutput into master

This adds basic file output to the I/O thread. Currently, the input data for events that pass one of the trigger lines is copied into the output file but no additional banks are added.

This branch is based on the branch raaij_thboettc_dec_reports and modified to move the file output from the GPU threads to the I/O thread.

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