Formaline uses files that end in ccldeps to record dependencies for its tarballs. These files are used like ".d" dependency makefiles by the build system.
However since the files end in .ccldeps rather than .d and are in $SCRATCH rather than $BUILD they are not removed by a make sim-cleandeps.
This shows up if one eg moves a thorn from one arrangement to another since the ccldeps file will list a dependency on eg the interface.ccl file in the old location that can no longer be satisfied.
A workaround right now is to do a make sim-clean which clears out $SCRATCH but requires a full recompile.