Military courts would not handle crimes by "members of the security forces" that constituted "crimes against humanity, and crimes of genocide, forced disappearances, extrajudicial executions, sexual violence, torture and forced displacement."
This means that, for example, so-called 'false positives' would be tried by the ordinary courts and not by the military.
The bill also includes a paragraph that gives the prosecutor, in coordination with the military courts, a year to review "all cases against members of the security forces" and move "to the military justice those that do not come within the jurisdiction of the ordinary courts." [Rough Google translation]El Espectador has additional coverage here. Columbia Reports says "[t]he bill still has to be passed by the House of Representatives and be approved in four debates before the end of the congressional term in June of next year."