Added an chnnum override switch so that one can specify a chnnum if they know that an IQ file has the wrong chnnum value stored in it.
Changed many files so that the scf can be written to the rawacf file.
Added the final bits of code needed to write the SCF.
Fixed comment errors and some minor compilation errors.
Merge branch 'make_raw_for_wrong_chnnum' into testing
Modifications to that self-clutter estimates can be written to rawacf files.