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I have the following dune file which compiles fine from command line with dune but not under merlin:
(executable
 (name main)
 ; workaround for https://github.com/ocaml/dune/issues/3636
 (flags (:standard -w -27 -I +../cerberus/frontend))) 
In merling-log buffer I see:
"ocaml": {
    "include_dirs": [
      "/home/lord/src/cheri-c-semantics/ubfinder/+../cerberus/frontend"
    ],
If I change it to full path:
(executable
 (name main)
 ; workaround for https://github.com/ocaml/dune/issues/3636
 (flags (:standard -w -27 -I /home/lord/.opam/cerberus/lib/cerberus/frontend))) 
it shows in log:
  "ocaml": {
    "include_dirs": [ "/home/lord/.opam/cerberus/lib/cerberus/frontend" ],
and compiles fine.
It looks like an issue with + handling with -I