CNN recently ran a report on the truce that the Salvadoran government reached with the MS-13 and 18th street gang in El Salvador: Church’s pact with the devil.
It's pretty clear that the Funes government was behind the truce between the gangs. Colindres and Mijango have been working as mediators between the gangs but they were hand selected by Munguia Payes and Funes. While it might have made sense to deny government involvement during the first few weeks/months, there's no need to deny it any longer.