Fcl expansion doesn't handle absolute path includes.
#includes in fcl files don't work if the included file is specified using an absolute path (starting with either "/" or "./").
#1 Updated by Rob Kutschke about 6 years ago
For what it's worth, Mu2e does not consider this a bug. We explicitly requested this feature. I believe (Chris/Marc can confirm) that It is possible to change this on a per experiment basis.
Do you know about the environment variable FHICL_FILE_PATH ? Mu2e felt that this provided enough flexibility for development and enough control to ensure that people did not sneak uncontrolled configurations into production jobs.