@tclune @amdasilva was having a talk with @AgilentGCMS and he said that the input files for the ACG get "installed" (probably because they end in .rc) and therefore end up in the experiment's RC directory which can be confusing.
This is purely a cmake issue and very low hanging fruit. No reason these files should be "installed" as they are not runtime. This should be easy enough to do via some cmake and/or perhaps an extensions change for these files.
Food for thought.