Here is what happened.
In v3.1.0 a new feature was added.
If the same name appears in different directories in the project, they can can be disambiguated and compiled.
dir1
-- Rules.mk
-- FOO.PGM: foo.rpgle
dir2
-- Rules.mk
-- FOO.MODULE: foo.rpgle
in this case both FOO.PGM and FOO.MODULE could be uniquely built.
Unfortunately this required a change to the compile command to specify the directory qualifying the source file.
i.e.
makei compile -f foo.rpgle is ambiguous in this case. So you have to say makei compile -f dir2/foo.rpgle
But this causes a different set of problems. It is a breaking change for VS Code tooling and what people type.
We will roll this change back so we stop breaking the tools and people's use.
@SanjulaGanepola thank you for pointing this out