We have a big project which looks like this one.
playground.zip

$ tree
.
├── dune-workspace
└── dune_exe
    ├── demo.opam
    ├── dune
    ├── dune-project
    ├── lib.ml
    ├── sub_exe
    │   ├── dune
    │   └── sub.ml
    ├── test.ml
    └── test2.ml

While compiling with dune build @all, we obtain a .merlin file in dune_exe. This .merlin file contains -open Dune__exe. If I understand correctly, this module is generated by dune to wrap binaries. Unfortunately it seems to confuse merlin. Whenever we run a command with the "classic" merlin protocol in, we obtain an error because of a missing Dune__exe:

/home/louis/.opam/a/bin/ocamlmerlin single type-enclosing -protocol sexp -verbosity 0 -filename /long/path/to/a/file/test.ml -position 6:8 -index 0 < test.ml
((assoc) (class . "error") (value . "Unbound module Dune__exe") (notifications) (timing (assoc) (clock . 45) (cpu . 39) (query . 2) (pp . 0) (reader . 11) (ppx . 17) (typer . 10) (error . 0)))

In sub_exe/.merlin there is also -open Dune__exe, but no problem for merlin there.

It appears that merlin doesn't have this issue when used through ocaml-lsp, which is curious.

Unfortunately I couldn't manage to create a small example to replicate the error. I didn't find a way to trigger dune to generate the -open Dune__exe bit of the .merlin on a small case.

What I find suspicious is that dune generates only one Dune_exe module if I understand correctly (taken from our real repo, not the code shared above)

$ find ../_build/default/| rg une__exe\.c
../_build/default/some_project/sub_exe/.sub.eobjs/byte/dune__exe.cmi
../_build/default/some_project/sub_exe/.sub.eobjs/byte/dune__exe.cmt
../_build/default/some_project/sub_exe/.sub.eobjs/byte/dune__exe.cmo

And for the test binary, dune__exe is used as a prefix

$ find ../_build/default/| rg une__exe | rg test
../_build/default/some_project/.test.eobjs/byte/dune__exe__Test.cmt
../_build/default/some_project/.test.eobjs/byte/dune__exe__Test.cmo
../_build/default/some_project/.test.eobjs/byte/dune__exe__Test.cmi
../_build/default/some_project/.test.eobjs/dune__exe__Test.impl.all-deps

Specifications

• Version of dune (output of dune --version): 2.2.0 and 2.5.1
• Version of ocaml (output of ocamlc --version): 4.09.0
• Operating system (distribution and version): debian 10