diff --git a/doc/changes/10422.md b/doc/changes/10422.md
new file mode 100644
index 00000000000..b298dd1a8b8
--- /dev/null
+++ b/doc/changes/10422.md
@@ -0,0 +1,7 @@
+- `dune ocaml-merlin`: communicate additional directives `SOURCE_ROOT`,
+  `UNIT_NAME` (the actual name with wrapping) and `INDEX` with the paths to the
+  index(es). (#10422, @voodoos)
+
+- Add a new alias `@ocaml-index` that uses the `ocaml-index` binary to generate
+  indexes that can be read by tools such as Merlin to provide project-wide
+  references search. (#10422, @voodoos)
diff --git a/doc/reference/aliases.rst b/doc/reference/aliases.rst
index 098b32a1418..504e4499611 100644
--- a/doc/reference/aliases.rst
+++ b/doc/reference/aliases.rst
@@ -76,6 +76,7 @@ Some aliases are defined and managed by Dune itself:
        :caption: Checks
 
        aliases/check
+       aliases/ocaml-index
        aliases/runtest
        aliases/fmt
        aliases/lint
diff --git a/doc/reference/aliases/check.rst b/doc/reference/aliases/check.rst
index f27baa8c17c..1e2c8de8305 100644
--- a/doc/reference/aliases/check.rst
+++ b/doc/reference/aliases/check.rst
@@ -6,3 +6,6 @@ work correctly. For example, it will build ``*.cmi``, ``*.cmt``, and ``*.cmti``
 files so that Merlin and ``ocaml-lsp-server`` can be used in the project.
 It is also useful in the development loop because it will catch compilation
 errors without executing expensive operations such as linking executables.
+
+.. seealso:: :doc:`ocaml-index` for a fast feedback loop that
+   also indexes the project.
diff --git a/doc/reference/aliases/ocaml-index.rst b/doc/reference/aliases/ocaml-index.rst
new file mode 100644
index 00000000000..a68c5fbc47e
--- /dev/null
+++ b/doc/reference/aliases/ocaml-index.rst
@@ -0,0 +1,9 @@
+@ocaml-index
+============
+
+This alias corresponds to the set of targets necessary for development tools to
+provide project-wide queries such as "get all references of this value". These
+targets are indexes built using the required `ocaml-index` binary. Since this
+alias also incudes the ``*.cmi``, ``*.cmt``, and ``*.cmti`` files usually built
+by ``check``, it can be used in most projects as a replacement to get a fast
+feedback loop while maintaining the indexes up-to-date.
diff --git a/src/dune_rules/alias0.ml b/src/dune_rules/alias0.ml
index 5b61ee6e8ba..f93c313dd33 100644
--- a/src/dune_rules/alias0.ml
+++ b/src/dune_rules/alias0.ml
@@ -14,5 +14,6 @@ let doc_json = standard "doc-json"
 let doc_new = standard "doc-new"
 let check = standard "check"
 let install = standard "install"
+let ocaml_index = standard "ocaml-index"
 let runtest = standard "runtest"
 let all = standard "all"
diff --git a/src/dune_rules/alias0.mli b/src/dune_rules/alias0.mli
index 95635594d35..ed42b67ec10 100644
--- a/src/dune_rules/alias0.mli
+++ b/src/dune_rules/alias0.mli
@@ -11,6 +11,7 @@ val lint : Name.t
 val private_doc : Name.t
 val doc_new : Name.t
 val check : Name.t
+val ocaml_index : Name.t
 val install : Name.t
 val runtest : Name.t
 val all : Name.t
diff --git a/src/dune_rules/exe.ml b/src/dune_rules/exe.ml
index c29612cc599..368529a84fe 100644
--- a/src/dune_rules/exe.ml
+++ b/src/dune_rules/exe.ml
@@ -363,6 +363,10 @@ let build_and_link_many
   =
   let open Memo.O in
   let* () = Module_compilation.build_all cctx in
+  let* () =
+    Memo.when_ (Compilation_context.bin_annot cctx) (fun () ->
+      Ocaml_index.cctx_rules cctx)
+  in
   link_many
     ?link_args
     ?o_files
diff --git a/src/dune_rules/exe_rules.ml b/src/dune_rules/exe_rules.ml
index 536ee728ab9..cfd1eebb403 100644
--- a/src/dune_rules/exe_rules.ml
+++ b/src/dune_rules/exe_rules.ml
@@ -182,6 +182,7 @@ let executables_rules
   let lib_config = ocaml.lib_config in
   let stdlib_dir = lib_config.stdlib_dir in
   let* requires_compile = Compilation_context.requires_compile cctx in
+  let* requires_link = Compilation_context.requires_link cctx in
   let* dep_graphs =
     (* Building an archive for foreign stubs, we link the corresponding object
        files directly to improve perf. *)
@@ -265,7 +266,7 @@ let executables_rules
   in
   ( cctx
   , Merlin.make
-      ~requires:requires_compile
+      ~requires:requires_link
       ~stdlib_dir
       ~flags
       ~modules
diff --git a/src/dune_rules/gen_rules.ml b/src/dune_rules/gen_rules.ml
index 4ddf3d06f29..6259c12ecc6 100644
--- a/src/dune_rules/gen_rules.ml
+++ b/src/dune_rules/gen_rules.ml
@@ -353,6 +353,7 @@ let gen_project_rules =
     let+ () = Install_rules.gen_project_rules sctx project
     and+ () = Odoc.gen_project_rules sctx project
     and+ () = Odoc_new.gen_project_rules sctx project
+    and+ () = Ocaml_index.project_rule sctx project
     and+ () =
       let version = 2, 8 in
       match Dune_project.allow_approximate_merlin project with
diff --git a/src/dune_rules/lib_rules.ml b/src/dune_rules/lib_rules.ml
index 82f729dd807..1c5fcb9caf4 100644
--- a/src/dune_rules/lib_rules.ml
+++ b/src/dune_rules/lib_rules.ml
@@ -579,6 +579,7 @@ let library_rules
   let scope = Compilation_context.scope cctx in
   let* requires_compile = Compilation_context.requires_compile cctx in
   let ocaml = Compilation_context.ocaml cctx in
+  let* requires_link = Compilation_context.requires_link cctx in
   let stdlib_dir = ocaml.lib_config.stdlib_dir in
   let top_sorted_modules =
     let impl_only = Modules.With_vlib.impl_only modules in
@@ -607,6 +608,9 @@ let library_rules
     info
   in
   let+ () =
+    Memo.when_ (Compilation_context.bin_annot cctx) (fun () ->
+      Ocaml_index.cctx_rules cctx)
+  and+ () =
     Memo.when_
       (not (Library.is_virtual lib))
       (fun () -> setup_build_archives lib ~lib_info ~top_sorted_modules ~cctx ~expander)
@@ -631,7 +635,7 @@ let library_rules
   in
   ( cctx
   , Merlin.make
-      ~requires:requires_compile
+      ~requires:requires_link
       ~stdlib_dir
       ~flags
       ~modules
diff --git a/src/dune_rules/merlin/merlin.ml b/src/dune_rules/merlin/merlin.ml
index fa70393ae8e..900ef0bd483 100644
--- a/src/dune_rules/merlin/merlin.ml
+++ b/src/dune_rules/merlin/merlin.ml
@@ -48,20 +48,26 @@ module Processed = struct
   (* Most of the configuration is shared across a same lib/exe... *)
   type config =
     { stdlib_dir : Path.t option
+    ; source_root : Path.t
     ; obj_dirs : Path.Set.t
     ; src_dirs : Path.Set.t
     ; flags : string list
     ; extensions : string option Ml_kind.Dict.t list
+    ; indexes : Path.t list
     }
 
-  let dyn_of_config { stdlib_dir; obj_dirs; src_dirs; flags; extensions } =
+  let dyn_of_config
+    { stdlib_dir; source_root; obj_dirs; src_dirs; flags; extensions; indexes }
+    =
     let open Dyn in
     record
       [ "stdlib_dir", option Path.to_dyn stdlib_dir
+      ; "source_root", Path.to_dyn source_root
       ; "obj_dirs", Path.Set.to_dyn obj_dirs
       ; "src_dirs", Path.Set.to_dyn src_dirs
       ; "flags", list string flags
       ; "extensions", list (Ml_kind.Dict.to_dyn (Dyn.option string)) extensions
+      ; "indexes", list Path.to_dyn indexes
       ]
   ;;
 
@@ -100,16 +106,18 @@ module Processed = struct
     type nonrec t = t
 
     let name = "merlin-conf"
-    let version = 4
+    let version = 5
     let to_dyn _ = Dyn.String "Use [dune ocaml dump-dot-merlin] instead"
 
     let test_example () =
       { config =
           { stdlib_dir = None
+          ; source_root = Path.Source.root |> Path.source
           ; obj_dirs = Path.Set.empty
           ; src_dirs = Path.Set.empty
           ; flags = [ "-x" ]
           ; extensions = [ { Ml_kind.Dict.intf = None; impl = Some "ext" } ]
+          ; indexes = []
           }
       ; per_file_config = Path.Build.Map.empty
       ; pp_config =
@@ -149,16 +157,24 @@ module Processed = struct
     | None, None -> None
   ;;
 
-  let to_sexp ~opens ~pp ~reader { stdlib_dir; obj_dirs; src_dirs; flags; extensions } =
+  let to_sexp
+    ~unit_name
+    ~opens
+    ~pp
+    ~reader
+    { stdlib_dir; source_root; obj_dirs; src_dirs; flags; extensions; indexes }
+    =
     let make_directive tag value = Sexp.List [ Atom tag; value ] in
     let make_directive_of_path tag path =
       make_directive tag (Sexp.Atom (serialize_path path))
     in
+    let index_files = List.map indexes ~f:(fun p -> make_directive_of_path "INDEX" p) in
     let stdlib_dir =
       match stdlib_dir with
       | None -> []
       | Some stdlib_dir -> [ make_directive_of_path "STDLIB" stdlib_dir ]
     in
+    let source_root = [ make_directive_of_path "SOURCE_ROOT" source_root ] in
     let exclude_query_dir = [ Sexp.List [ Atom "EXCLUDE_QUERY_DIR" ] ] in
     let obj_dirs = Path.Set.to_list_map obj_dirs ~f:(make_directive_of_path "B") in
     let src_dirs = Path.Set.to_list_map src_dirs ~f:(make_directive_of_path "S") in
@@ -184,6 +200,7 @@ module Processed = struct
           (Sexp.List (Ocaml_flags.open_flags opens |> List.map ~f:(fun x -> Sexp.Atom x)))
         :: flags
     in
+    let unit_name = [ make_directive "UNIT_NAME" (Sexp.Atom unit_name) ] in
     let suffixes =
       List.filter_map extensions ~f:(fun x ->
         let open Option.O in
@@ -199,7 +216,17 @@ module Processed = struct
     in
     Sexp.List
       (List.concat
-         [ stdlib_dir; exclude_query_dir; obj_dirs; src_dirs; flags; suffixes; reader ])
+         [ index_files
+         ; stdlib_dir
+         ; source_root
+         ; exclude_query_dir
+         ; obj_dirs
+         ; src_dirs
+         ; flags
+         ; unit_name
+         ; suffixes
+         ; reader
+         ])
   ;;
 
   let quote_for_dot_merlin s =
@@ -215,15 +242,26 @@ module Processed = struct
     if String.need_quoting s then Filename.quote s else s
   ;;
 
-  let to_dot_merlin stdlib_dir pp_configs flags obj_dirs src_dirs extensions =
+  let to_dot_merlin
+    stdlib_dir
+    source_root
+    pp_configs
+    flags
+    obj_dirs
+    src_dirs
+    extensions
+    indexes
+    =
     let b = Buffer.create 256 in
     let printf = Printf.bprintf b in
     let print = Buffer.add_string b in
     print "EXCLUDE_QUERY_DIR\n";
     Option.iter stdlib_dir ~f:(fun stdlib_dir ->
       printf "STDLIB %s\n" (serialize_path stdlib_dir));
+    printf "SOURCE_ROOT %s\n" (serialize_path source_root);
     Path.Set.iter obj_dirs ~f:(fun p -> printf "B %s\n" (serialize_path p));
     Path.Set.iter src_dirs ~f:(fun p -> printf "S %s\n" (serialize_path p));
+    List.iter indexes ~f:(fun p -> printf "INDEX %s\n" (serialize_path p));
     List.iter extensions ~f:(fun x ->
       Option.iter (get_ext x) ~f:(fun (impl, intf) ->
         printf "SUFFIX %s" (Printf.sprintf "%s %s" impl intf)));
@@ -265,7 +303,8 @@ module Processed = struct
            Path.Build.Map.find per_file_config (remove_extension file))
     in
     let pp = Module_name.Per_item.get pp_config (Module.name module_) in
-    to_sexp ~opens ~pp ~reader config
+    let unit_name = Module_name.Unique.to_string (Module.obj_name module_) in
+    to_sexp ~unit_name ~opens ~pp ~reader config
   ;;
 
   let print_file path =
@@ -275,8 +314,9 @@ module Processed = struct
       let pp_one (source, { module_; opens; reader }) =
         let open Pp.O in
         let name = Module.name module_ in
+        let unit_name = Module_name.Unique.to_string (Module.obj_name module_) in
         let pp = Module_name.Per_item.get pp_config name in
-        let sexp = to_sexp ~reader ~opens ~pp config in
+        let sexp = to_sexp ~unit_name ~reader ~opens ~pp config in
         Pp.hvbox
           (Pp.textf "%s: %s" (Module_name.to_string name) (Path.Build.to_string source))
         ++ Pp.newline
@@ -295,7 +335,7 @@ module Processed = struct
     | Error msg -> Printf.eprintf "%s\n" msg
     | Ok [] -> Printf.eprintf "No merlin configuration found.\n"
     | Ok (init :: tl) ->
-      let pp_configs, obj_dirs, src_dirs, flags, extensions =
+      let pp_configs, obj_dirs, src_dirs, flags, extensions, indexes =
         (* We merge what is easy to merge and ignore the rest *)
         List.fold_left
           tl
@@ -304,30 +344,42 @@ module Processed = struct
             , init.config.obj_dirs
             , init.config.src_dirs
             , [ init.config.flags ]
-            , init.config.extensions )
+            , init.config.extensions
+            , init.config.indexes )
           ~f:
             (fun
-              (acc_pp, acc_obj, acc_src, acc_flags, acc_ext)
+              (acc_pp, acc_obj, acc_src, acc_flags, acc_ext, acc_indexes)
               { per_file_config = _
               ; pp_config
-              ; config = { stdlib_dir = _; obj_dirs; src_dirs; flags; extensions }
+              ; config =
+                  { stdlib_dir = _
+                  ; source_root = _
+                  ; obj_dirs
+                  ; src_dirs
+                  ; flags
+                  ; extensions
+                  ; indexes
+                  }
               }
             ->
             ( pp_config :: acc_pp
             , Path.Set.union acc_obj obj_dirs
             , Path.Set.union acc_src src_dirs
             , flags :: acc_flags
-            , extensions @ acc_ext ))
+            , extensions @ acc_ext
+            , indexes @ acc_indexes ))
       in
       Printf.printf
         "%s\n"
         (to_dot_merlin
            init.config.stdlib_dir
+           init.config.source_root
            pp_configs
            flags
            obj_dirs
            src_dirs
-           extensions)
+           extensions
+           indexes)
   ;;
 end
 
@@ -579,11 +631,19 @@ module Unprocessed = struct
                        obj_dir_of_lib `Public mode (Lib_info.obj_dir info)
                      in
                      Path.Set.add obj_dirs public_cmi_dir )))
-      in
+      and+ indexes = Action_builder.of_memo (Ocaml_index.context_indexes sctx) in
       let src_dirs =
         Path.Set.union src_dirs (Path.Set.of_list_map ~f:Path.source more_src_dirs)
       in
-      { Processed.stdlib_dir; src_dirs; obj_dirs; flags; extensions }
+      let source_root = Path.Source.root |> Path.source in
+      { Processed.stdlib_dir
+      ; source_root
+      ; src_dirs
+      ; obj_dirs
+      ; flags
+      ; extensions
+      ; indexes
+      }
     and+ pp_config = pp_config t (Super_context.context sctx) ~expander in
     let per_file_config =
       (* And copy for each module the resulting pp flags *)
diff --git a/src/dune_rules/merlin/ocaml_index.ml b/src/dune_rules/merlin/ocaml_index.ml
new file mode 100644
index 00000000000..58909d7ba18
--- /dev/null
+++ b/src/dune_rules/merlin/ocaml_index.ml
@@ -0,0 +1,107 @@
+open Import
+
+let ocaml_index sctx ~dir =
+  Super_context.resolve_program ~loc:None ~dir sctx "ocaml-index"
+;;
+
+let index_path_in_obj_dir obj_dir =
+  let dir = Obj_dir.obj_dir obj_dir in
+  Path.Build.relative dir "cctx.ocaml-index"
+;;
+
+let project_index ~build_dir = Path.Build.relative build_dir "project.ocaml-index"
+
+let cctx_rules cctx =
+  (* Indexing is performed by the external binary [ocaml-index] which performs
+     full shape reduction to compute the actual definition of all the elements in
+     the typedtree. This step is therefore dependent on all the cmts of those
+     definitions are used by all the cmts of modules in this cctx. *)
+  let sctx = Compilation_context.super_context cctx in
+  let dir = Compilation_context.dir cctx in
+  let aggregate =
+    let obj_dir = Compilation_context.obj_dir cctx in
+    let fn = index_path_in_obj_dir obj_dir in
+    let additional_libs =
+      let open Resolve.Memo.O in
+      let+ non_compile_libs =
+        (* The indexer relies on the load_path of cmt files. When
+           [implicit_transitive_deps] is set to [false] some necessary paths will
+           be missing.These are passed to the indexer with the `-I` flag.
+
+           The implicit transitive libs correspond to the set:
+           (requires_link \ req_compile) *)
+        let* req_link = Compilation_context.requires_link cctx in
+        let+ req_compile = Compilation_context.requires_compile cctx in
+        List.filter req_link ~f:(fun l -> not (List.exists req_compile ~f:(Lib.equal l)))
+      in
+      Lib_flags.L.include_flags non_compile_libs (Lib_mode.Ocaml Byte)
+    in
+    let context_dir =
+      Compilation_context.context cctx
+      |> Context.name
+      |> Context_name.build_dir
+      |> Path.build
+    in
+    let modules_deps =
+      let cm_kind = Lib_mode.Cm_kind.(Ocaml Cmi) in
+      (* We only index occurrences in user-written modules *)
+      Compilation_context.modules cctx
+      |> Modules.With_vlib.drop_vlib
+      |> Modules.fold_user_written ~init:[] ~f:(fun module_ acc ->
+        let cmts =
+          [ Ml_kind.Intf; Impl ]
+          |> List.filter_map ~f:(fun ml_kind ->
+            Obj_dir.Module.cmt_file obj_dir ~ml_kind ~cm_kind module_
+            |> Option.map ~f:Path.build)
+        in
+        List.rev_append cmts acc)
+    in
+    Command.run_dyn_prog
+      ~dir:context_dir
+      (ocaml_index sctx ~dir)
+      [ A "aggregate"
+      ; A "-o"
+      ; Target fn
+      ; Deps modules_deps
+      ; Dyn (Resolve.Memo.read additional_libs)
+      ]
+  in
+  Super_context.add_rule sctx ~dir aggregate
+;;
+
+let context_indexes sctx =
+  let open Memo.O in
+  let ctx = Super_context.context sctx in
+  Context.name ctx
+  |> Dune_load.dune_files
+  >>| Dune_file.fold_static_stanzas ~init:[] ~f:(fun dune_file stanza acc ->
+    let obj =
+      let dir =
+        let build_dir = Context.build_dir ctx in
+        Path.Build.append_source build_dir (Dune_file.dir dune_file)
+      in
+      match Stanza.repr stanza with
+      | Executables.T exes | Tests.T { exes; _ } -> Some (Executables.obj_dir ~dir exes)
+      | Library.T lib -> Some (Library.obj_dir ~dir lib)
+      | _ -> None
+    in
+    match obj with
+    | None -> acc
+    | Some obj_dir -> Path.build (index_path_in_obj_dir obj_dir) :: acc)
+;;
+
+let project_rule sctx project =
+  let open Memo.O in
+  let ocaml_index_alias =
+    let dir =
+      let build_dir =
+        let ctx = Super_context.context sctx in
+        Context.build_dir ctx
+      in
+      Path.Build.append_source build_dir @@ Dune_project.root project
+    in
+    Alias.make Alias0.ocaml_index ~dir
+  in
+  let* indexes = context_indexes sctx in
+  Rules.Produce.Alias.add_deps ocaml_index_alias (Action_builder.paths_existing @@ indexes)
+;;
diff --git a/src/dune_rules/merlin/ocaml_index.mli b/src/dune_rules/merlin/ocaml_index.mli
new file mode 100644
index 00000000000..a9d7a9480fc
--- /dev/null
+++ b/src/dune_rules/merlin/ocaml_index.mli
@@ -0,0 +1,26 @@
+open Import
+
+(** This module provides support for the [ocaml-uideps] indexing tool. Its role
+    is to index every value in the project by their definition in order for
+    language server to be able to fetch project-wide occurrences.
+
+    Indexing all definitions usages is a two step process:
+
+    - first, for all compilation contexts we generate the uideps for all the
+      modules in that cctx in the corresponding obj_dir.
+    - then we aggregate all these separate indexes into a unique one. *)
+
+val project_index : build_dir:Path.Build.t -> Path.Build.t
+
+(** [cctx_rules cctx] sets the rules needed to generate the indexes for every
+    module in the compilation context [cctx] and aggregate them in a
+    [cctx.uideps] index covering the whole compilation context. *)
+val cctx_rules : Compilation_context.t -> unit Memo.t
+
+(** [context_indexes] lists all the available cctx.ocaml-index files in the
+    given context *)
+val context_indexes : Super_context.t -> Path.t list Memo.t
+
+(** [project_rule] adds a rule that will aggregate all the generated indexes
+    into one global, project-wide, index *)
+val project_rule : Super_context.t -> Dune_project.t -> unit Memo.t
diff --git a/src/dune_rules/module_compilation.ml b/src/dune_rules/module_compilation.ml
index 6b5f82150c6..2679731999f 100644
--- a/src/dune_rules/module_compilation.ml
+++ b/src/dune_rules/module_compilation.ml
@@ -191,7 +191,14 @@ let build_cm
          let fn =
            Option.value_exn (Obj_dir.Module.cmt_file obj_dir m ~cm_kind ~ml_kind)
          in
-         fn :: other_targets, A "-bin-annot")
+         let annots =
+           [ "-bin-annot" ]
+           @
+           if Version.supports_bin_annot_occurrences ocaml.version
+           then [ "-bin-annot-occurrences" ]
+           else []
+         in
+         fn :: other_targets, As annots)
        else other_targets, Command.Args.empty
    in
    let opaque_arg : _ Command.Args.t =
diff --git a/src/ocaml/version.ml b/src/ocaml/version.ml
index 09c06cdb765..fba7b9e1a25 100644
--- a/src/ocaml/version.ml
+++ b/src/ocaml/version.ml
@@ -28,3 +28,4 @@ let has_bigarray_library version = version < (5, 0, 0)
 let supports_alerts version = version >= (4, 8, 0)
 let has_sandboxed_otherlibs version = version >= (5, 0, 0)
 let has_META_files version = version >= (5, 0, 0)
+let supports_bin_annot_occurrences version = version >= (5, 2, 0)
diff --git a/src/ocaml/version.mli b/src/ocaml/version.mli
index 8291d77deb2..f7da69ad2b1 100644
--- a/src/ocaml/version.mli
+++ b/src/ocaml/version.mli
@@ -73,3 +73,6 @@ val has_sandboxed_otherlibs : t -> bool
 
 (** Whether the compiler distributes META files independently of ocamlfind *)
 val has_META_files : t -> bool
+
+(** Whether the compiler supports occurrences indexation *)
+val supports_bin_annot_occurrences : t -> bool
diff --git a/test/blackbox-tests/test-cases/describe/aliases.t/run.t b/test/blackbox-tests/test-cases/describe/aliases.t/run.t
index f3f2a0d7a28..d166a9adba8 100644
--- a/test/blackbox-tests/test-cases/describe/aliases.t/run.t
+++ b/test/blackbox-tests/test-cases/describe/aliases.t/run.t
@@ -8,6 +8,7 @@ In an empty dune project, the following aliases are available.
   all
   default
   fmt
+  ocaml-index
 
 User defined aliases can be added to a dune file. These should be picked up by
 the command.
@@ -22,6 +23,7 @@ the command.
   default
   fmt
   foo
+  ocaml-index
 
 Aliases in subdirectories should not be picked up.
 
@@ -36,6 +38,7 @@ Aliases in subdirectories should not be picked up.
   default
   fmt
   foo
+  ocaml-index
 
 But checking the subdirectory it should be available.
 
@@ -58,6 +61,7 @@ Adding an OCaml library will introduce OCaml specific aliases:
   default
   doc-private
   fmt
+  ocaml-index
 
 Adding a cram test will introduce an alias with the name of the test and also
 introduce the runtest alias:
@@ -70,6 +74,7 @@ bbb
   default
   fmt
   mytest
+  ocaml-index
   runtest
 
 We can also show aliases in multiple directories at once:
@@ -80,6 +85,7 @@ We can also show aliases in multiple directories at once:
   default
   fmt
   mytest
+  ocaml-index
   runtest
   
   subdir:
@@ -97,6 +103,7 @@ Including those in the _build/ directory:
   default
   fmt
   mytest
+  ocaml-index
   runtest
   
   _build/default:
@@ -104,6 +111,7 @@ Including those in the _build/ directory:
   default
   fmt
   mytest
+  ocaml-index
   runtest
 
 These are context sensitive:
@@ -123,4 +131,5 @@ These are context sensitive:
   default
   fmt
   mytest
+  ocaml-index
   runtest
diff --git a/test/blackbox-tests/test-cases/dune b/test/blackbox-tests/test-cases/dune
index 55d2ada31c4..3165c0740af 100644
--- a/test/blackbox-tests/test-cases/dune
+++ b/test/blackbox-tests/test-cases/dune
@@ -9,7 +9,8 @@
    ../utils/melc_stdlib_prefix.exe
    ../utils/refmt.exe
    ../utils/webserver_oneshot.exe
-   ../utils/sherlodoc.exe)))
+   ../utils/sherlodoc.exe
+   ../utils/ocaml_index.exe)))
 
 (cram
  (applies_to pp-cwd)
diff --git a/test/blackbox-tests/test-cases/github2206.t/run.t b/test/blackbox-tests/test-cases/github2206.t/run.t
index 976772d7dc0..1848c413d07 100644
--- a/test/blackbox-tests/test-cases/github2206.t/run.t
+++ b/test/blackbox-tests/test-cases/github2206.t/run.t
@@ -2,9 +2,15 @@ copy_files would break the generation of the preprocessing flags
   $ dune build copy_files/.merlin-conf/exe-foo
   $ dune ocaml merlin dump-config $PWD/copy_files |
   > grep -B 1 -A 0 "pp"
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.pp.eobjs/cctx.ocaml-index)
+  --
    (FLG
     (-pp
      $TESTCASE_ROOT/_build/default/pp.exe))
+  --
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.pp.eobjs/cctx.ocaml-index)
   --
    (FLG
     (-pp
diff --git a/test/blackbox-tests/test-cases/melange/merlin-compile-flags.t b/test/blackbox-tests/test-cases/melange/merlin-compile-flags.t
index 3bd56c798ff..0cbb9959435 100644
--- a/test/blackbox-tests/test-cases/melange/merlin-compile-flags.t
+++ b/test/blackbox-tests/test-cases/melange/merlin-compile-flags.t
@@ -18,12 +18,12 @@ Show that the merlin config knows about melange.compile_flags
   $ dune build @check
 
   $ dune ocaml merlin dump-config "$PWD" | grep -i "+42"
-     +42)))
-     +42)))
-     +42)))
-     +42)))
-     +42)))
-     +42)))
+     +42))
+     +42))
+     +42))
+     +42))
+     +42))
+     +42))
 
   $ cat >dune <<EOF
   > (melange.emit
@@ -35,10 +35,10 @@ Show that the merlin config knows about melange.compile_flags
   $ dune build @check
 
   $ dune ocaml merlin dump-config "$PWD" | grep -i "+42"
-     +42)))
-     +42)))
-     +42)))
-     +42)))
-     +42)))
-     +42)))
+     +42))
+     +42))
+     +42))
+     +42))
+     +42))
+     +42))
 
diff --git a/test/blackbox-tests/test-cases/melange/merlin.t b/test/blackbox-tests/test-cases/melange/merlin.t
index dba7817a04d..5781fa0ceab 100644
--- a/test/blackbox-tests/test-cases/melange/merlin.t
+++ b/test/blackbox-tests/test-cases/melange/merlin.t
@@ -23,20 +23,32 @@
   $ touch bar.ml $lib.ml
   $ dune build @check
   $ dune ocaml merlin dump-config "$PWD" | grep -i "$lib"
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
     $TESTCASE_ROOT/_build/default/.foo.objs/melange)
    (FLG (-open Foo__))
+   (UNIT_NAME foo__Bar))
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
     $TESTCASE_ROOT/_build/default/.foo.objs/melange)
    (FLG (-open Foo__))
+   (UNIT_NAME foo__Bar))
   Foo: _build/default/foo
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
     $TESTCASE_ROOT/_build/default/.foo.objs/melange)
    (FLG (-open Foo__))
+   (UNIT_NAME foo))
   Foo: _build/default/foo.ml
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
     $TESTCASE_ROOT/_build/default/.foo.objs/melange)
    (FLG (-open Foo__))
+   (UNIT_NAME foo))
   Foo__: _build/default/foo__
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
     $TESTCASE_ROOT/_build/default/.foo.objs/melange)
+   (UNIT_NAME foo__))
   Foo__: _build/default/foo__.ml-gen
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
     $TESTCASE_ROOT/_build/default/.foo.objs/melange)
+   (UNIT_NAME foo__))
 
 Paths to Melange stdlib appear in B and S entries without melange.emit stanza
 
@@ -70,6 +82,7 @@ Dump-dot-merlin includes the melange flags
   $ dune ocaml dump-dot-merlin $PWD
   EXCLUDE_QUERY_DIR
   STDLIB /MELC_STDLIB/melange
+  SOURCE_ROOT $TESTCASE_ROOT
   B /MELC_STDLIB/__private__/melange_mini_stdlib/melange/.public_cmi_melange
   B /MELC_STDLIB/melange
   B /MELC_STDLIB/melange
@@ -115,7 +128,13 @@ User ppx flags should appear in merlin config
 
   $ dune ocaml merlin dump-config $PWD | grep -v "(B "  | grep -v "(S "
   Bar: _build/default/bar
-  ((STDLIB /MELC_STDLIB/melange)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.fooppx.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /MELC_STDLIB/melange)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     /MELC_STDLIB/__private__/melange_mini_stdlib/melange/.public_cmi_melange)
@@ -139,9 +158,16 @@ User ppx flags should appear in merlin config
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo__Bar))
   Bar: _build/default/bar.ml
-  ((STDLIB /MELC_STDLIB/melange)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.fooppx.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /MELC_STDLIB/melange)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     /MELC_STDLIB/__private__/melange_mini_stdlib/melange/.public_cmi_melange)
@@ -165,9 +191,16 @@ User ppx flags should appear in merlin config
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo__Bar))
   Foo: _build/default/foo
-  ((STDLIB /MELC_STDLIB/melange)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.fooppx.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /MELC_STDLIB/melange)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     /MELC_STDLIB/__private__/melange_mini_stdlib/melange/.public_cmi_melange)
@@ -190,9 +223,16 @@ User ppx flags should appear in merlin config
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo))
   Foo: _build/default/foo.ml-gen
-  ((STDLIB /MELC_STDLIB/melange)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.fooppx.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /MELC_STDLIB/melange)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     /MELC_STDLIB/__private__/melange_mini_stdlib/melange/.public_cmi_melange)
@@ -215,9 +255,16 @@ User ppx flags should appear in merlin config
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo))
   Fooppx: _build/default/fooppx
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.fooppx.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.fooppx.objs/byte)
@@ -230,9 +277,16 @@ User ppx flags should appear in merlin config
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME fooppx))
   Fooppx: _build/default/fooppx.ml
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.fooppx.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.fooppx.objs/byte)
@@ -245,4 +299,5 @@ User ppx flags should appear in merlin config
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME fooppx))
diff --git a/test/blackbox-tests/test-cases/merlin/alt-context.t b/test/blackbox-tests/test-cases/merlin/alt-context.t
index 4808c567d61..24444d6e69c 100644
--- a/test/blackbox-tests/test-cases/merlin/alt-context.t
+++ b/test/blackbox-tests/test-cases/merlin/alt-context.t
@@ -66,12 +66,16 @@ Request config for file in alt context without using --context
 Request config for file in alt context using --context
 
   $ printf '(4:File%d:%s)' ${#FILE2} $FILE2 | dune ocaml-merlin --context alt | dune format-dune-file | grep -i "$lib2" | sed 's/^[^:]*:[^:]*://'
+  $TESTCASE_ROOT/_build/alt/.bar.objs/cctx.ocaml-index)
   $TESTCASE_ROOT/_build/alt/.bar.objs/byte)
+  bar))
 
 Request config for default context without using --context
 
   $ printf '(4:File%d:%s)' ${#FILE1} $FILE1 | dune ocaml-merlin | dune format-dune-file | grep -i "$lib1" | sed 's/^[^:]*:[^:]*://'
+  $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
   $TESTCASE_ROOT/_build/default/.foo.objs/byte)
+  foo))
 
 Request config for default context using --context
 
diff --git a/test/blackbox-tests/test-cases/merlin/default-based-context.t/run.t b/test/blackbox-tests/test-cases/merlin/default-based-context.t/run.t
index c0f5f55d8f1..1498b216403 100644
--- a/test/blackbox-tests/test-cases/merlin/default-based-context.t/run.t
+++ b/test/blackbox-tests/test-cases/merlin/default-based-context.t/run.t
@@ -23,7 +23,11 @@ If Merlin field is absent, default context is chosen
 
   $ dune ocaml merlin dump-config "$PWD"
   Foo: _build/default/foo
-  ((STDLIB OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -36,9 +40,14 @@ If Merlin field is absent, default context is chosen
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo))
   Foo: _build/default/foo.ml
-  ((STDLIB OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -51,7 +60,8 @@ If Merlin field is absent, default context is chosen
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo))
 
 If Merlin field is present, this context is chosen
 
@@ -76,7 +86,11 @@ If Merlin field is present, this context is chosen
 
   $ dune ocaml merlin dump-config "$PWD"
   Foo: _build/cross/foo
-  ((STDLIB OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/cross/.foo.objs/cctx.ocaml-index)
+   (STDLIB OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/cross/.foo.objs/byte)
@@ -89,9 +103,14 @@ If Merlin field is present, this context is chosen
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo))
   Foo: _build/cross/foo.ml
-  ((STDLIB OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/cross/.foo.objs/cctx.ocaml-index)
+   (STDLIB OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/cross/.foo.objs/byte)
@@ -104,7 +123,8 @@ If Merlin field is present, this context is chosen
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo))
 
 If `generate_merlin_rules` field is present, rules are generated even if merlin
 is disabled in that context
@@ -132,7 +152,11 @@ is disabled in that context
 
   $ dune ocaml merlin dump-config "$PWD"
   Foo: _build/default/foo
-  ((STDLIB OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -145,9 +169,14 @@ is disabled in that context
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo))
   Foo: _build/default/foo.ml
-  ((STDLIB OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -160,4 +189,5 @@ is disabled in that context
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo))
diff --git a/test/blackbox-tests/test-cases/merlin/dialect.t/run.t b/test/blackbox-tests/test-cases/merlin/dialect.t/run.t
index 017b3386ac5..c72b1df5e34 100644
--- a/test/blackbox-tests/test-cases/merlin/dialect.t/run.t
+++ b/test/blackbox-tests/test-cases/merlin/dialect.t/run.t
@@ -9,55 +9,100 @@ CRAM sanitization
   $ dune build ./exe/.merlin-conf/exe-x --profile release
   $ dune ocaml merlin dump-config $PWD/exe
   X: _build/default/exe/x
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.x.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/melange/.x_mel.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/exe/.x.eobjs/byte)
    (S
     $TESTCASE_ROOT/exe)
    (FLG (-w -40 -g))
+   (UNIT_NAME dune__exe__X)
    (SUFFIX ".mlx .mlx"))
   X: _build/default/exe/x.mlx
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.x.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/melange/.x_mel.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/exe/.x.eobjs/byte)
    (S
     $TESTCASE_ROOT/exe)
    (FLG (-w -40 -g))
+   (UNIT_NAME dune__exe__X)
    (SUFFIX ".mlx .mlx")
    (READER (mlx)))
   X: _build/default/exe/x.mlx.mli
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.x.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/melange/.x_mel.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/exe/.x.eobjs/byte)
    (S
     $TESTCASE_ROOT/exe)
    (FLG (-w -40 -g))
+   (UNIT_NAME dune__exe__X)
    (SUFFIX ".mlx .mlx"))
 
 CRAM sanitization
   $ dune build ./lib/.merlin-conf/lib-x --profile release
   $ dune ocaml merlin dump-config $PWD/lib
   X: _build/default/lib/x
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.x.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/melange/.x_mel.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/lib/.x.objs/byte)
    (S
     $TESTCASE_ROOT/lib)
    (FLG (-w -40 -g))
+   (UNIT_NAME x)
    (SUFFIX ".mlx .mlx")
    (READER (mlx)))
   X: _build/default/lib/x.mlx
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.x.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/melange/.x_mel.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/lib/.x.objs/byte)
    (S
     $TESTCASE_ROOT/lib)
    (FLG (-w -40 -g))
+   (UNIT_NAME x)
    (SUFFIX ".mlx .mlx")
    (READER (mlx)))
 
@@ -65,7 +110,15 @@ CRAM sanitization
   $ dune build ./melange/.merlin-conf/lib-x_mel --profile release
   $ dune ocaml merlin dump-config $PWD/melange
   X_mel: _build/default/melange/x_mel
-  ((STDLIB lib/melange/melange)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.x.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/melange/.x_mel.objs/cctx.ocaml-index)
+   (STDLIB lib/melange/melange)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     lib/melange/__private__/melange_mini_stdlib/melange/.public_cmi_melange)
@@ -80,10 +133,19 @@ CRAM sanitization
    (S
     $TESTCASE_ROOT/melange)
    (FLG (-w -40 -g))
+   (UNIT_NAME x_mel)
    (SUFFIX ".mlx .mlx")
    (READER (mlx)))
   X_mel: _build/default/melange/x_mel.mlx
-  ((STDLIB lib/melange/melange)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.x.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/melange/.x_mel.objs/cctx.ocaml-index)
+   (STDLIB lib/melange/melange)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     lib/melange/__private__/melange_mini_stdlib/melange/.public_cmi_melange)
@@ -98,5 +160,6 @@ CRAM sanitization
    (S
     $TESTCASE_ROOT/melange)
    (FLG (-w -40 -g))
+   (UNIT_NAME x_mel)
    (SUFFIX ".mlx .mlx")
    (READER (mlx)))
diff --git a/test/blackbox-tests/test-cases/merlin/dump-dot-merlin.t/run.t b/test/blackbox-tests/test-cases/merlin/dump-dot-merlin.t/run.t
index 4f0167631e4..631ec11e9ba 100644
--- a/test/blackbox-tests/test-cases/merlin/dump-dot-merlin.t/run.t
+++ b/test/blackbox-tests/test-cases/merlin/dump-dot-merlin.t/run.t
@@ -5,15 +5,21 @@
   $ dune ocaml dump-dot-merlin src\ with\ spaces
   EXCLUDE_QUERY_DIR
   STDLIB /OCAMLC_WHERE
+  SOURCE_ROOT $TESTCASE_ROOT
   B $TESTCASE_ROOT/_build/default/src with spaces/.foo.eobjs/byte
   S $TESTCASE_ROOT/src with spaces
+  INDEX $TESTCASE_ROOT/_build/default/p p/.pp.eobjs/cctx.ocaml-index
+  INDEX $TESTCASE_ROOT/_build/default/src with spaces/.foo.eobjs/cctx.ocaml-index
   # FLG -pp ''\''$TESTCASE_ROOT/_build/default/p p/pp.exe'\'''
   # FLG -w @1..3@5..28@30..39@43@46..47@49..57@61..62-40 -strict-sequence -strict-formats -short-paths -keep-locs -g
   
   $ dune ocaml dump-dot-merlin "p p"
   EXCLUDE_QUERY_DIR
   STDLIB /OCAMLC_WHERE
+  SOURCE_ROOT $TESTCASE_ROOT
   B $TESTCASE_ROOT/_build/default/p p/.pp.eobjs/byte
   S $TESTCASE_ROOT/p p
+  INDEX $TESTCASE_ROOT/_build/default/p p/.pp.eobjs/cctx.ocaml-index
+  INDEX $TESTCASE_ROOT/_build/default/src with spaces/.foo.eobjs/cctx.ocaml-index
   # FLG -w @1..3@5..28@30..39@43@46..47@49..57@61..62-40 -strict-sequence -strict-formats -short-paths -keep-locs -g
   
diff --git a/test/blackbox-tests/test-cases/merlin/future-syntax.t b/test/blackbox-tests/test-cases/merlin/future-syntax.t
index c70ccca2e6f..9d9cb6338b1 100644
--- a/test/blackbox-tests/test-cases/merlin/future-syntax.t
+++ b/test/blackbox-tests/test-cases/merlin/future-syntax.t
@@ -18,26 +18,41 @@
   $ dune build ./.merlin-conf/exe-pp_future_syntax --profile release
   $ dune ocaml merlin dump-config .
   Pp_future_syntax: _build/default/pp_future_syntax
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.pp_future_syntax.eobjs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.pp_future_syntax.eobjs/byte)
    (S
     $TESTCASE_ROOT)
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME dune__exe__Pp_future_syntax))
   Pp_future_syntax: _build/default/pp_future_syntax.ml
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.pp_future_syntax.eobjs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.pp_future_syntax.eobjs/byte)
    (S
     $TESTCASE_ROOT)
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME dune__exe__Pp_future_syntax))
   Pp_future_syntax: _build/default/pp_future_syntax.mli
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.pp_future_syntax.eobjs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.pp_future_syntax.eobjs/byte)
    (S
     $TESTCASE_ROOT)
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME dune__exe__Pp_future_syntax))
diff --git a/test/blackbox-tests/test-cases/merlin/github1946.t/run.t b/test/blackbox-tests/test-cases/merlin/github1946.t/run.t
index ffa28575f75..6ae6ba318f4 100644
--- a/test/blackbox-tests/test-cases/merlin/github1946.t/run.t
+++ b/test/blackbox-tests/test-cases/merlin/github1946.t/run.t
@@ -7,7 +7,17 @@ in the same dune file, but require different ppx specifications
   $ dune build @all --profile release
   $ dune ocaml merlin dump-config $PWD
   Usesppx1: _build/default/usesppx1
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.usesppx2.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/.usesppx1.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx1/.ppx1.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx2/.ppx2.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.usesppx1.objs/byte)
@@ -19,9 +29,20 @@ in the same dune file, but require different ppx specifications
      --as-ppx
      --cookie
      'library-name="usesppx1"'"))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME usesppx1))
   Usesppx1: _build/default/usesppx1.ml-gen
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.usesppx2.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/.usesppx1.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx1/.ppx1.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx2/.ppx2.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.usesppx1.objs/byte)
@@ -33,9 +54,20 @@ in the same dune file, but require different ppx specifications
      --as-ppx
      --cookie
      'library-name="usesppx1"'"))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME usesppx1))
   Usesppx2: _build/default/usesppx2
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.usesppx2.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/.usesppx1.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx1/.ppx1.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx2/.ppx2.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.usesppx2.objs/byte)
@@ -47,9 +79,20 @@ in the same dune file, but require different ppx specifications
      --as-ppx
      --cookie
      'library-name="usesppx2"'"))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME usesppx2))
   Usesppx2: _build/default/usesppx2.ml-gen
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.usesppx2.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/.usesppx1.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx1/.ppx1.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx2/.ppx2.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.usesppx2.objs/byte)
@@ -61,4 +104,5 @@ in the same dune file, but require different ppx specifications
      --as-ppx
      --cookie
      'library-name="usesppx2"'"))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME usesppx2))
diff --git a/test/blackbox-tests/test-cases/merlin/github4125.t/run.t b/test/blackbox-tests/test-cases/merlin/github4125.t/run.t
index 39b8b2fd915..4b87e69091f 100644
--- a/test/blackbox-tests/test-cases/merlin/github4125.t/run.t
+++ b/test/blackbox-tests/test-cases/merlin/github4125.t/run.t
@@ -23,7 +23,11 @@ We call `$(opam switch show)` so that this test always uses an existing switch
 
   $ dune ocaml merlin dump-config "$PWD"
   Foo: _build/cross/foo
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/cross/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/cross/.foo.objs/byte)
@@ -36,9 +40,14 @@ We call `$(opam switch show)` so that this test always uses an existing switch
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo))
   Foo: _build/cross/foo.ml
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/cross/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/cross/.foo.objs/byte)
@@ -51,4 +60,5 @@ We call `$(opam switch show)` so that this test always uses an existing switch
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo))
diff --git a/test/blackbox-tests/test-cases/merlin/github759.t/run.t b/test/blackbox-tests/test-cases/merlin/github759.t/run.t
index 286f4180c8b..b4fcb10ad9a 100644
--- a/test/blackbox-tests/test-cases/merlin/github759.t/run.t
+++ b/test/blackbox-tests/test-cases/merlin/github759.t/run.t
@@ -4,58 +4,88 @@
   $ dune build foo.cma --profile release
   $ dune ocaml merlin dump-config $PWD
   Foo: _build/default/foo
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
    (S
     $TESTCASE_ROOT)
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME foo))
   Foo: _build/default/foo.ml-gen
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
    (S
     $TESTCASE_ROOT)
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME foo))
 
   $ rm -f .merlin
   $ dune build foo.cma --profile release
   $ dune ocaml merlin dump-config $PWD
   Foo: _build/default/foo
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
    (S
     $TESTCASE_ROOT)
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME foo))
   Foo: _build/default/foo.ml-gen
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
    (S
     $TESTCASE_ROOT)
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME foo))
 
   $ echo toto > .merlin
   $ dune build foo.cma --profile release
   $ dune ocaml merlin dump-config $PWD
   Foo: _build/default/foo
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
    (S
     $TESTCASE_ROOT)
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME foo))
   Foo: _build/default/foo.ml-gen
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
    (S
     $TESTCASE_ROOT)
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME foo))
diff --git a/test/blackbox-tests/test-cases/merlin/granularity.t b/test/blackbox-tests/test-cases/merlin/granularity.t
index ec8bdb63cd1..fd339cafffe 100644
--- a/test/blackbox-tests/test-cases/merlin/granularity.t
+++ b/test/blackbox-tests/test-cases/merlin/granularity.t
@@ -117,13 +117,16 @@ Preprocessing:
 
 Is it expected that the suffix for implementation and interface is the same ?
   $ ./merlin_conf.sh pped.ml | tee pped.out
-  ((?:STDLIB?:/OCAMLC_WHERE
+  ((?:INDEX?:$TESTCASE_ROOT/_build/default/.test.eobjs/cctx.ocaml-index
+  (?:STDLIB?:/OCAMLC_WHERE
+  (?:SOURCE_ROOT?:$TESTCASE_ROOT
   (?:EXCLUDE_QUERY_DIR
   (?:B?:$TESTCASE_ROOT/_build/default/.test.eobjs/byte
   (?:S?:$TESTCASE_ROOT
   (?:FLG(?:-open?:Dune__exe)
   (?:FLG(?:-pp?:$TESTCASE_ROOT/_build/default/pp.sh)
   (?:FLG(?:-w?:@1..3@5..28@31..39@43@46..47@49..57@61..62@67@69-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-no-strict-formats?:-g)
+  (?:UNIT_NAME?:dune__exe__Pped
   (?:SUFFIX?:.mlx .mlx))
 
   $ ./merlin_conf.sh pped.mli | diff pped.out -
@@ -132,17 +135,20 @@ Melange:
 
 As expected, the reader is not communicated for the standard mli
   $ ./merlin_conf.sh mel.mli | tee mel.out
-  ((?:STDLIB?:/OCAMLC_WHERE
+  ((?:INDEX?:$TESTCASE_ROOT/_build/default/.test.eobjs/cctx.ocaml-index
+  (?:STDLIB?:/OCAMLC_WHERE
+  (?:SOURCE_ROOT?:$TESTCASE_ROOT
   (?:EXCLUDE_QUERY_DIR
   (?:B?:$TESTCASE_ROOT/_build/default/.test.eobjs/byte
   (?:S?:$TESTCASE_ROOT
   (?:FLG(?:-open?:Dune__exe)
   (?:FLG(?:-w?:@1..3@5..28@31..39@43@46..47@49..57@61..62@67@69-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-no-strict-formats?:-g)
+  (?:UNIT_NAME?:dune__exe__Mel
   (?:SUFFIX?:.mlx .mlx))
 
 The reader is set for the mlx file
   $ ./merlin_conf.sh mel.mlx | diff mel.out -
-  7c7,8
+  10c10,11
   < (?:SUFFIX?:.mlx .mlx))
   \ No newline at end of file
   ---
@@ -161,12 +167,15 @@ found, then it'll make a guess that the file was preprocessed into a file with
 .ml extension:
 
   $ ./merlin_conf.sh cppomod.cppo.ml | tee cppomod.out
-  ((?:STDLIB?:/OCAMLC_WHERE
+  ((?:INDEX?:$TESTCASE_ROOT/_build/default/.test.eobjs/cctx.ocaml-index
+  (?:STDLIB?:/OCAMLC_WHERE
+  (?:SOURCE_ROOT?:$TESTCASE_ROOT
   (?:EXCLUDE_QUERY_DIR
   (?:B?:$TESTCASE_ROOT/_build/default/.test.eobjs/byte
   (?:S?:$TESTCASE_ROOT
   (?:FLG(?:-open?:Dune__exe)
   (?:FLG(?:-w?:@1..3@5..28@31..39@43@46..47@49..57@61..62@67@69-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-no-strict-formats?:-g)
+  (?:UNIT_NAME?:dune__exe__Cppomod
   (?:SUFFIX?:.mlx .mlx))
 
   $ ./merlin_conf.sh cppomod.ml | diff cppomod.out -
@@ -180,12 +189,15 @@ And with unconventional extension:
 such files) 
 We could expect dune to get the wrongext module configuration
   $ ./merlin_conf.sh wrongext.cppo.cml | tee wrongext.out
-  ((?:STDLIB?:/OCAMLC_WHERE
+  ((?:INDEX?:$TESTCASE_ROOT/_build/default/.test.eobjs/cctx.ocaml-index
+  (?:STDLIB?:/OCAMLC_WHERE
+  (?:SOURCE_ROOT?:$TESTCASE_ROOT
   (?:EXCLUDE_QUERY_DIR
   (?:B?:$TESTCASE_ROOT/_build/default/.test.eobjs/byte
   (?:S?:$TESTCASE_ROOT
   (?:FLG(?:-open?:Dune__exe)
   (?:FLG(?:-w?:@1..3@5..28@31..39@43@46..47@49..57@61..62@67@69-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-no-strict-formats?:-g)
+  (?:UNIT_NAME?:dune__exe__Wrongext
   (?:SUFFIX?:.mlx .mlx))
 
 We also have generated.ml and generatedx.mlx promoted:
@@ -195,19 +207,25 @@ We also have generated.ml and generatedx.mlx promoted:
 
 It should be possible to get its merlin configuration as well:
   $ ./merlin_conf.sh generated.ml
-  ((?:STDLIB?:/OCAMLC_WHERE
+  ((?:INDEX?:$TESTCASE_ROOT/_build/default/.test.eobjs/cctx.ocaml-index
+  (?:STDLIB?:/OCAMLC_WHERE
+  (?:SOURCE_ROOT?:$TESTCASE_ROOT
   (?:EXCLUDE_QUERY_DIR
   (?:B?:$TESTCASE_ROOT/_build/default/.test.eobjs/byte
   (?:S?:$TESTCASE_ROOT
   (?:FLG(?:-open?:Dune__exe)
   (?:FLG(?:-w?:@1..3@5..28@31..39@43@46..47@49..57@61..62@67@69-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-no-strict-formats?:-g)
+  (?:UNIT_NAME?:dune__exe__Generated
   (?:SUFFIX?:.mlx .mlx))
   $ ./merlin_conf.sh generatedx.mlx
-  ((?:STDLIB?:/OCAMLC_WHERE
+  ((?:INDEX?:$TESTCASE_ROOT/_build/default/.test.eobjs/cctx.ocaml-index
+  (?:STDLIB?:/OCAMLC_WHERE
+  (?:SOURCE_ROOT?:$TESTCASE_ROOT
   (?:EXCLUDE_QUERY_DIR
   (?:B?:$TESTCASE_ROOT/_build/default/.test.eobjs/byte
   (?:S?:$TESTCASE_ROOT
   (?:FLG(?:-open?:Dune__exe)
   (?:FLG(?:-w?:@1..3@5..28@31..39@43@46..47@49..57@61..62@67@69-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-no-strict-formats?:-g)
+  (?:UNIT_NAME?:dune__exe__Generatedx
   (?:SUFFIX?:.mlx .mlx
   (?:READER(?:mlx)))
diff --git a/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/bin/dune b/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/bin/dune
new file mode 100644
index 00000000000..95d07f5d928
--- /dev/null
+++ b/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/bin/dune
@@ -0,0 +1,3 @@
+(executable
+ (name main)
+ (libraries lib1))
\ No newline at end of file
diff --git a/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/bin/main.ml b/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/bin/main.ml
new file mode 100644
index 00000000000..2f5fb3b592d
--- /dev/null
+++ b/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/bin/main.ml
@@ -0,0 +1 @@
+type t = Lib1.t
\ No newline at end of file
diff --git a/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/dune-project b/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/dune-project
new file mode 100644
index 00000000000..f390b5360ef
--- /dev/null
+++ b/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/dune-project
@@ -0,0 +1,2 @@
+(lang dune 2.0)
+(implicit_transitive_deps false)
\ No newline at end of file
diff --git a/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/run.t b/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/run.t
new file mode 100644
index 00000000000..a4c084111ad
--- /dev/null
+++ b/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/run.t
@@ -0,0 +1,33 @@
+  $ stdlib="$(ocamlc -where)"
+  $ export BUILD_PATH_PREFIX_MAP="/STDLIB=$stdlib:$BUILD_PATH_PREFIX_MAP"
+
+  $ dune build @check
+
+FIXME: Merlin must be able to locate the definitions of values coming from an
+implicit transitive dependency, even when `implicit-transitive-dependency` is
+set to `false`. They should be part of the source path returned by the
+configuration.
+
+In this test the dependencies are as follow:
+main -> lib1 -> lib2 -> stdlib
+
+  $ FILE=$PWD/bin/main.ml
+  $ printf "(4:File%d:%s)" ${#FILE} $FILE | dune ocaml-merlin |
+  > sed -E "s/[[:digit:]]+:/\?:/g" | tr '(' '\n' | grep ":S?"
+  ?:S?:/STDLIB)
+  ?:S?:$TESTCASE_ROOT/bin)
+  ?:S?:$TESTCASE_ROOT/src/lib1)
+  ?:S?:$TESTCASE_ROOT/src/lib2)
+
+  $ FILE=$PWD/src/lib1/lib1.ml
+  $ printf "(4:File%d:%s)" ${#FILE} $FILE | dune ocaml-merlin |
+  > sed -E "s/[[:digit:]]+:/\?:/g" | tr '(' '\n' | grep ":S?"
+  ?:S?:/STDLIB)
+  ?:S?:$TESTCASE_ROOT/src/lib1)
+  ?:S?:$TESTCASE_ROOT/src/lib2)
+
+  $ FILE=$PWD/src/lib2/lib2.ml
+  $ printf "(4:File%d:%s)" ${#FILE} $FILE | dune ocaml-merlin |
+  > sed -E "s/[[:digit:]]+:/\?:/g" | tr '(' '\n' | grep ":S?"
+  ?:S?:/STDLIB)
+  ?:S?:$TESTCASE_ROOT/src/lib2)
diff --git a/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/src/lib1/dune b/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/src/lib1/dune
new file mode 100644
index 00000000000..70976155582
--- /dev/null
+++ b/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/src/lib1/dune
@@ -0,0 +1,3 @@
+(library
+ (name lib1)
+ (libraries lib2))
diff --git a/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/src/lib1/lib1.ml b/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/src/lib1/lib1.ml
new file mode 100644
index 00000000000..8b4941c18c6
--- /dev/null
+++ b/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/src/lib1/lib1.ml
@@ -0,0 +1 @@
+include Lib2
diff --git a/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/src/lib2/dune b/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/src/lib2/dune
new file mode 100644
index 00000000000..eba0287a9dd
--- /dev/null
+++ b/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/src/lib2/dune
@@ -0,0 +1,3 @@
+(library
+ (name lib2)
+ (libraries unix))
diff --git a/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/src/lib2/lib2.ml b/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/src/lib2/lib2.ml
new file mode 100644
index 00000000000..e206be29b61
--- /dev/null
+++ b/test/blackbox-tests/test-cases/merlin/implicit-transitive-deps.t/src/lib2/lib2.ml
@@ -0,0 +1,3 @@
+type t = bool
+
+type r = Unix.error
\ No newline at end of file
diff --git a/test/blackbox-tests/test-cases/merlin/include-subdirs-qualified.t b/test/blackbox-tests/test-cases/merlin/include-subdirs-qualified.t
index 834f28c3694..0500114f1f0 100644
--- a/test/blackbox-tests/test-cases/merlin/include-subdirs-qualified.t
+++ b/test/blackbox-tests/test-cases/merlin/include-subdirs-qualified.t
@@ -22,7 +22,11 @@
   $ dune build .merlin-conf/lib-foo
   $ dune ocaml merlin dump-config .
   Foo: _build/default/foo
-  ((STDLIB /OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -39,9 +43,14 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo))
   Foo: _build/default/foo.ml-gen
-  ((STDLIB /OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -58,9 +67,14 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo))
   Foo__Groupintf__: _build/default/foo__Groupintf__
-  ((STDLIB /OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -77,9 +91,14 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo__Groupintf__))
   Foo__Groupintf__: _build/default/foo__Groupintf__.ml-gen
-  ((STDLIB /OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -96,9 +115,14 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo__Groupintf__))
   Utils: _build/default/foo__Utils
-  ((STDLIB /OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -115,9 +139,14 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo__Utils))
   Utils: _build/default/foo__Utils.ml-gen
-  ((STDLIB /OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -134,9 +163,14 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo__Utils))
   Calc: _build/default/groupintf/calc
-  ((STDLIB /OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -154,9 +188,14 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo__Groupintf__Calc))
   Calc: _build/default/groupintf/calc.ml
-  ((STDLIB /OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -174,9 +213,14 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo__Groupintf__Calc))
   Groupintf: _build/default/groupintf/groupintf
-  ((STDLIB /OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -194,9 +238,14 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo__Groupintf))
   Groupintf: _build/default/groupintf/groupintf.ml
-  ((STDLIB /OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -214,9 +263,14 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo__Groupintf))
   Main: _build/default/main
-  ((STDLIB /OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -234,9 +288,14 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo__Main))
   Main: _build/default/main.ml
-  ((STDLIB /OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -254,9 +313,14 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo__Main))
   Calc: _build/default/utils/calc
-  ((STDLIB /OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -274,9 +338,14 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo__Utils__Calc))
   Calc: _build/default/utils/calc.ml
-  ((STDLIB /OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -294,5 +363,6 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo__Utils__Calc))
   $ dune ocaml merlin dump-config utils
diff --git a/test/blackbox-tests/test-cases/merlin/instrumentation.t/run.t b/test/blackbox-tests/test-cases/merlin/instrumentation.t/run.t
index 2fea5f64a9f..b7b121b3979 100644
--- a/test/blackbox-tests/test-cases/merlin/instrumentation.t/run.t
+++ b/test/blackbox-tests/test-cases/merlin/instrumentation.t/run.t
@@ -9,7 +9,19 @@ up a project with instrumentation and testing checking the merlin config.
   $ dune build --instrument-with hello ./lib/.merlin-conf/lib-foo ./lib/.merlin-conf/lib-bar --profile release
   $ dune ocaml merlin dump-config $PWD/lib
   Bar: _build/default/lib/bar
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.hello.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.hello_ppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/lib/.bar.objs/byte)
@@ -21,9 +33,22 @@ up a project with instrumentation and testing checking the merlin config.
     $TESTCASE_ROOT/lib/subdir)
    (S
     $TESTCASE_ROOT/ppx)
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME bar))
   Bar: _build/default/lib/bar.ml-gen
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.hello.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.hello_ppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/lib/.bar.objs/byte)
@@ -35,9 +60,22 @@ up a project with instrumentation and testing checking the merlin config.
     $TESTCASE_ROOT/lib/subdir)
    (S
     $TESTCASE_ROOT/ppx)
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME bar))
   File: _build/default/lib/subdir/file
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.hello.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.hello_ppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/lib/.bar.objs/byte)
@@ -50,9 +88,22 @@ up a project with instrumentation and testing checking the merlin config.
    (S
     $TESTCASE_ROOT/ppx)
    (FLG (-open Bar))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME bar__File))
   File: _build/default/lib/subdir/file.ml
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.hello.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.hello_ppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/lib/.bar.objs/byte)
@@ -65,9 +116,22 @@ up a project with instrumentation and testing checking the merlin config.
    (S
     $TESTCASE_ROOT/ppx)
    (FLG (-open Bar))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME bar__File))
   Foo: _build/default/lib/foo
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.hello.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.hello_ppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/lib/.foo.objs/byte)
@@ -79,9 +143,22 @@ up a project with instrumentation and testing checking the merlin config.
     $TESTCASE_ROOT/lib/subdir)
    (S
     $TESTCASE_ROOT/ppx)
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME foo))
   Foo: _build/default/lib/foo.ml-gen
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.hello.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.hello_ppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/lib/.foo.objs/byte)
@@ -93,9 +170,22 @@ up a project with instrumentation and testing checking the merlin config.
     $TESTCASE_ROOT/lib/subdir)
    (S
     $TESTCASE_ROOT/ppx)
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME foo))
   Privmod: _build/default/lib/privmod
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.hello.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.hello_ppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/lib/.foo.objs/byte)
@@ -108,9 +198,22 @@ up a project with instrumentation and testing checking the merlin config.
    (S
     $TESTCASE_ROOT/ppx)
    (FLG (-open Foo))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME foo__Privmod))
   Privmod: _build/default/lib/privmod.ml
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.hello.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.hello_ppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/lib/.foo.objs/byte)
@@ -123,4 +226,5 @@ up a project with instrumentation and testing checking the merlin config.
    (S
     $TESTCASE_ROOT/ppx)
    (FLG (-open Foo))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME foo__Privmod))
diff --git a/test/blackbox-tests/test-cases/merlin/merlin-from-subdir.t/run.t b/test/blackbox-tests/test-cases/merlin/merlin-from-subdir.t/run.t
index 3895364d430..97c2408a288 100644
--- a/test/blackbox-tests/test-cases/merlin/merlin-from-subdir.t/run.t
+++ b/test/blackbox-tests/test-cases/merlin/merlin-from-subdir.t/run.t
@@ -8,7 +8,13 @@ We build the project
 Verify that merlin configuration was generated...
   $ dune ocaml merlin dump-config $PWD
   Test: _build/default/test
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.test.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -25,9 +31,16 @@ Verify that merlin configuration was generated...
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME dune__exe__Test))
   Test: _build/default/test.ml
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.test.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -44,9 +57,16 @@ Verify that merlin configuration was generated...
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME dune__exe__Test))
   Foo: _build/default/foo
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.test.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -61,9 +81,16 @@ Verify that merlin configuration was generated...
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo))
   Foo: _build/default/foo.ml
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.test.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -78,7 +105,8 @@ Verify that merlin configuration was generated...
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo))
 
 ...but not in the sub-folder whose content was copied
   $ dune ocaml merlin dump-config $PWD/411
@@ -88,7 +116,7 @@ Now we check that both querying from the root and the subfolder works
   $ FILE411=$PWD/411/test.ml
 
   $ printf "(4:File%d:%s)" ${#FILE} $FILE | dune ocaml-merlin | sed -E "s/[[:digit:]]+:/\?:/g"
-  ((?:STDLIB?:/OCAMLC_WHERE)(?:EXCLUDE_QUERY_DIR)(?:B?:$TESTCASE_ROOT/_build/default/.foo.objs/byte)(?:S?:$TESTCASE_ROOT)(?:S?:$TESTCASE_ROOT/411)(?:FLG(?:-w?:@1..3@5..28@30..39@43@46..47@49..57@61..62-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-g)))
+  ((?:INDEX?:$TESTCASE_ROOT/_build/default/.test.eobjs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)(?:STDLIB?:/OCAMLC_WHERE)(?:SOURCE_ROOT?:$TESTCASE_ROOT)(?:EXCLUDE_QUERY_DIR)(?:B?:$TESTCASE_ROOT/_build/default/.foo.objs/byte)(?:S?:$TESTCASE_ROOT)(?:S?:$TESTCASE_ROOT/411)(?:FLG(?:-w?:@1..3@5..28@30..39@43@46..47@49..57@61..62-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-g))(?:UNIT_NAME?:foo))
 
   $ printf "(4:File%d:%s)" ${#FILE411} $FILE411 | dune ocaml-merlin | sed -E "s/[[:digit:]]+:/\?:/g"
-  ((?:STDLIB?:/OCAMLC_WHERE)(?:EXCLUDE_QUERY_DIR)(?:B?:$TESTCASE_ROOT/_build/default/.foo.objs/byte)(?:B?:$TESTCASE_ROOT/_build/default/.test.eobjs/byte)(?:S?:$TESTCASE_ROOT)(?:S?:$TESTCASE_ROOT/411)(?:FLG(?:-w?:@1..3@5..28@30..39@43@46..47@49..57@61..62-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-g)))
+  ((?:INDEX?:$TESTCASE_ROOT/_build/default/.test.eobjs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)(?:STDLIB?:/OCAMLC_WHERE)(?:SOURCE_ROOT?:$TESTCASE_ROOT)(?:EXCLUDE_QUERY_DIR)(?:B?:$TESTCASE_ROOT/_build/default/.foo.objs/byte)(?:B?:$TESTCASE_ROOT/_build/default/.test.eobjs/byte)(?:S?:$TESTCASE_ROOT)(?:S?:$TESTCASE_ROOT/411)(?:FLG(?:-w?:@1..3@5..28@30..39@43@46..47@49..57@61..62-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-g))(?:UNIT_NAME?:dune__exe__Test))
diff --git a/test/blackbox-tests/test-cases/merlin/merlin-tests.t/run.t b/test/blackbox-tests/test-cases/merlin/merlin-tests.t/run.t
index c164517d918..cf9a880957d 100644
--- a/test/blackbox-tests/test-cases/merlin/merlin-tests.t/run.t
+++ b/test/blackbox-tests/test-cases/merlin/merlin-tests.t/run.t
@@ -14,7 +14,23 @@ CRAM sanitization
   $ dune build ./exe/.merlin-conf/exe-x --profile release
   $ dune ocaml merlin dump-config $PWD/exe
   X: _build/default/exe/x
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/exes/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp-with-expand/.foobar.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.fooppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_findlib/publicfoo)
@@ -31,9 +47,26 @@ CRAM sanitization
    (FLG
     (-pp
      $TESTCASE_ROOT/_build/default/pp/pp.exe))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME x))
   X: _build/default/exe/x.ml
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/exes/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp-with-expand/.foobar.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.fooppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_findlib/publicfoo)
@@ -50,12 +83,29 @@ CRAM sanitization
    (FLG
     (-pp
      $TESTCASE_ROOT/_build/default/pp/pp.exe))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME x))
 
   $ dune build ./lib/.merlin-conf/lib-foo ./lib/.merlin-conf/lib-bar --profile release
   $ dune ocaml merlin dump-config $PWD/lib
   Bar: _build/default/lib/bar
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/exes/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp-with-expand/.foobar.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.fooppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/lib/.bar.objs/byte)
@@ -69,9 +119,26 @@ CRAM sanitization
      --as-ppx
      --cookie
      'library-name="bar"'"))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME bar))
   Bar: _build/default/lib/bar.ml-gen
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/exes/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp-with-expand/.foobar.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.fooppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/lib/.bar.objs/byte)
@@ -85,9 +152,26 @@ CRAM sanitization
      --as-ppx
      --cookie
      'library-name="bar"'"))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME bar))
   File: _build/default/lib/subdir/file
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/exes/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp-with-expand/.foobar.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.fooppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/lib/.bar.objs/byte)
@@ -102,9 +186,26 @@ CRAM sanitization
      --as-ppx
      --cookie
      'library-name="bar"'"))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME bar__File))
   File: _build/default/lib/subdir/file.ml
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/exes/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp-with-expand/.foobar.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.fooppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/lib/.bar.objs/byte)
@@ -119,9 +220,26 @@ CRAM sanitization
      --as-ppx
      --cookie
      'library-name="bar"'"))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME bar__File))
   Foo: _build/default/lib/foo
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/exes/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp-with-expand/.foobar.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.fooppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_findlib/publicfoo)
@@ -139,9 +257,26 @@ CRAM sanitization
      --as-ppx
      --cookie
      'library-name="foo"'"))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME foo))
   Foo: _build/default/lib/foo.ml-gen
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/exes/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp-with-expand/.foobar.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.fooppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_findlib/publicfoo)
@@ -159,9 +294,26 @@ CRAM sanitization
      --as-ppx
      --cookie
      'library-name="foo"'"))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME foo))
   Privmod: _build/default/lib/privmod
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/exes/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp-with-expand/.foobar.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.fooppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_findlib/publicfoo)
@@ -180,9 +332,26 @@ CRAM sanitization
      --as-ppx
      --cookie
      'library-name="foo"'"))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME foo__Privmod))
   Privmod: _build/default/lib/privmod.ml
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/exes/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp-with-expand/.foobar.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.fooppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_findlib/publicfoo)
@@ -201,7 +370,8 @@ CRAM sanitization
      --as-ppx
      --cookie
      'library-name="foo"'"))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME foo__Privmod))
 
 Make sure a ppx directive is generated (if not, the [grep ppx] step fails)
   $ dune ocaml merlin dump-config $PWD/lib | grep ppx > /dev/null
@@ -211,7 +381,23 @@ Make sure pp flag is correct and variables are expanded
   $ dune build ./pp-with-expand/.merlin-conf/exe-foobar --profile release
   $ dune ocaml merlin dump-config $PWD/pp-with-expand
   Foobar: _build/default/pp-with-expand/foobar
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/exes/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp-with-expand/.foobar.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.fooppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/pp-with-expand/.foobar.eobjs/byte)
@@ -221,9 +407,26 @@ Make sure pp flag is correct and variables are expanded
     (-pp
      "$TESTCASE_ROOT/_build/default/pp/pp.exe
      -nothing"))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME foobar))
   Foobar: _build/default/pp-with-expand/foobar.ml
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/exes/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp-with-expand/.foobar.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.fooppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/pp-with-expand/.foobar.eobjs/byte)
@@ -233,13 +436,30 @@ Make sure pp flag is correct and variables are expanded
     (-pp
      "$TESTCASE_ROOT/_build/default/pp/pp.exe
      -nothing"))
-   (FLG (-w -40 -g)))
+   (FLG (-w -40 -g))
+   (UNIT_NAME foobar))
 
 Check hash of executables names if more than one
   $ dune build ./exes/.merlin-conf/exe-x-6562915302827c6dce0630390bfa68b7
   $ dune ocaml merlin dump-config $PWD/exes
   X: _build/default/exes/x
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/exes/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp-with-expand/.foobar.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.fooppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/exes/.x.eobjs/byte)
@@ -252,9 +472,26 @@ Check hash of executables names if more than one
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME x))
   X: _build/default/exes/x.ml
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/exes/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp-with-expand/.foobar.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.fooppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/exes/.x.eobjs/byte)
@@ -267,9 +504,26 @@ Check hash of executables names if more than one
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME x))
   Y: _build/default/exes/y
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/exes/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp-with-expand/.foobar.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.fooppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/exes/.x.eobjs/byte)
@@ -282,9 +536,26 @@ Check hash of executables names if more than one
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME y))
   Y: _build/default/exes/y.ml
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/exe/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/exes/.x.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.bar.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp-with-expand/.foobar.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/ppx/.fooppx.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/exes/.x.eobjs/byte)
@@ -297,4 +568,5 @@ Check hash of executables names if more than one
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME y))
diff --git a/test/blackbox-tests/test-cases/merlin/per-module-pp.t/run.t b/test/blackbox-tests/test-cases/merlin/per-module-pp.t/run.t
index 532a2f258a7..495b59dceaa 100644
--- a/test/blackbox-tests/test-cases/merlin/per-module-pp.t/run.t
+++ b/test/blackbox-tests/test-cases/merlin/per-module-pp.t/run.t
@@ -8,7 +8,13 @@ should appear only once since only Foo is using it.
 
   $ dune ocaml merlin dump-config $PWD
   Bar: _build/default/bar
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -21,9 +27,16 @@ should appear only once since only Foo is using it.
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME bar))
   Bar: _build/default/bar.ml
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -36,9 +49,16 @@ should appear only once since only Foo is using it.
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME bar))
   Foo: _build/default/foo
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -54,9 +74,16 @@ should appear only once since only Foo is using it.
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo))
   Foo: _build/default/foo.ml
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/pp/.pp.eobjs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.objs/byte)
@@ -72,4 +99,5 @@ should appear only once since only Foo is using it.
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo))
diff --git a/test/blackbox-tests/test-cases/merlin/server.t/run.t b/test/blackbox-tests/test-cases/merlin/server.t/run.t
index fd6f18b1717..505271236e6 100644
--- a/test/blackbox-tests/test-cases/merlin/server.t/run.t
+++ b/test/blackbox-tests/test-cases/merlin/server.t/run.t
@@ -8,11 +8,11 @@
   $ dune build @check
 
   $ printf "(4:File%d:%s)" ${#FILE} $FILE | dune ocaml-merlin | sed -E "s/[[:digit:]]+:/\?:/g"
-  ((?:STDLIB?:/OCAMLC_WHERE)(?:EXCLUDE_QUERY_DIR)(?:B?:$TESTCASE_ROOT/_build/default/.main.eobjs/byte)(?:B?:$TESTCASE_ROOT/_build/default/.mylib.objs/byte)(?:B?:$TESTCASE_ROOT/_build/default/.mylib3.objs/byte)(?:S?:$TESTCASE_ROOT)(?:FLG(?:-open?:Dune__exe))(?:FLG(?:-w?:@1..3@5..28@30..39@43@46..47@49..57@61..62-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-g)))
+  ((?:INDEX?:$TESTCASE_ROOT/_build/default/.not-a-module-name.eobjs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.main.eobjs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.mylib3.objs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.mylib.objs/cctx.ocaml-index)(?:STDLIB?:/OCAMLC_WHERE)(?:SOURCE_ROOT?:$TESTCASE_ROOT)(?:EXCLUDE_QUERY_DIR)(?:B?:$TESTCASE_ROOT/_build/default/.main.eobjs/byte)(?:B?:$TESTCASE_ROOT/_build/default/.mylib.objs/byte)(?:B?:$TESTCASE_ROOT/_build/default/.mylib3.objs/byte)(?:S?:$TESTCASE_ROOT)(?:FLG(?:-open?:Dune__exe))(?:FLG(?:-w?:@1..3@5..28@30..39@43@46..47@49..57@61..62-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-g))(?:UNIT_NAME?:dune__exe__Main))
 
   $ FILE=$PWD/lib3.ml
   $ printf "(4:File%d:%s)" ${#FILE} $FILE | dune ocaml-merlin | sed -E "s/[[:digit:]]+:/\?:/g"
-  ((?:STDLIB?:/OCAMLC_WHERE)(?:EXCLUDE_QUERY_DIR)(?:B?:$TESTCASE_ROOT/_build/default/.mylib.objs/byte)(?:B?:$TESTCASE_ROOT/_build/default/.mylib3.objs/byte)(?:S?:$TESTCASE_ROOT)(?:FLG(?:-open?:Mylib3))(?:FLG(?:-w?:@1..3@5..28@30..39@43@46..47@49..57@61..62-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-g)))
+  ((?:INDEX?:$TESTCASE_ROOT/_build/default/.not-a-module-name.eobjs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.main.eobjs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.mylib3.objs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.mylib.objs/cctx.ocaml-index)(?:STDLIB?:/OCAMLC_WHERE)(?:SOURCE_ROOT?:$TESTCASE_ROOT)(?:EXCLUDE_QUERY_DIR)(?:B?:$TESTCASE_ROOT/_build/default/.mylib.objs/byte)(?:B?:$TESTCASE_ROOT/_build/default/.mylib3.objs/byte)(?:S?:$TESTCASE_ROOT)(?:FLG(?:-open?:Mylib3))(?:FLG(?:-w?:@1..3@5..28@30..39@43@46..47@49..57@61..62-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-g))(?:UNIT_NAME?:mylib3__Lib3))
 
 If a file has a name of the kind `module_name.xx.xxx.ml/i`
 we consider it as ``module_name.ml/i`
@@ -20,24 +20,24 @@ This can be useful when some build scripts perform custom
 preprocessing and copy files around.
   $ FILE=lib3.foobar.ml
   $ printf "(4:File%d:%s)" ${#FILE} $FILE | dune ocaml-merlin | sed -E "s/[[:digit:]]+:/\?:/g"
-  ((?:STDLIB?:/OCAMLC_WHERE)(?:EXCLUDE_QUERY_DIR)(?:B?:$TESTCASE_ROOT/_build/default/.mylib.objs/byte)(?:B?:$TESTCASE_ROOT/_build/default/.mylib3.objs/byte)(?:S?:$TESTCASE_ROOT)(?:FLG(?:-open?:Mylib3))(?:FLG(?:-w?:@1..3@5..28@30..39@43@46..47@49..57@61..62-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-g)))
+  ((?:INDEX?:$TESTCASE_ROOT/_build/default/.not-a-module-name.eobjs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.main.eobjs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.mylib3.objs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.mylib.objs/cctx.ocaml-index)(?:STDLIB?:/OCAMLC_WHERE)(?:SOURCE_ROOT?:$TESTCASE_ROOT)(?:EXCLUDE_QUERY_DIR)(?:B?:$TESTCASE_ROOT/_build/default/.mylib.objs/byte)(?:B?:$TESTCASE_ROOT/_build/default/.mylib3.objs/byte)(?:S?:$TESTCASE_ROOT)(?:FLG(?:-open?:Mylib3))(?:FLG(?:-w?:@1..3@5..28@30..39@43@46..47@49..57@61..62-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-g))(?:UNIT_NAME?:mylib3__Lib3))
 
 If a directory has no configuration the configuration of its parent is used
 This can be useful when some build scripts copy files from subdirectories.
   $ FILE=foobar/lib3.foobar.ml
   $ printf "(4:File%d:%s)" ${#FILE} $FILE | dune ocaml-merlin | sed -E "s/[[:digit:]]+:/\?:/g"
-  ((?:STDLIB?:/OCAMLC_WHERE)(?:EXCLUDE_QUERY_DIR)(?:B?:$TESTCASE_ROOT/_build/default/.mylib.objs/byte)(?:B?:$TESTCASE_ROOT/_build/default/.mylib3.objs/byte)(?:S?:$TESTCASE_ROOT)(?:FLG(?:-open?:Mylib3))(?:FLG(?:-w?:@1..3@5..28@30..39@43@46..47@49..57@61..62-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-g)))
+  ((?:INDEX?:$TESTCASE_ROOT/_build/default/.not-a-module-name.eobjs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.main.eobjs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.mylib3.objs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.mylib.objs/cctx.ocaml-index)(?:STDLIB?:/OCAMLC_WHERE)(?:SOURCE_ROOT?:$TESTCASE_ROOT)(?:EXCLUDE_QUERY_DIR)(?:B?:$TESTCASE_ROOT/_build/default/.mylib.objs/byte)(?:B?:$TESTCASE_ROOT/_build/default/.mylib3.objs/byte)(?:S?:$TESTCASE_ROOT)(?:FLG(?:-open?:Mylib3))(?:FLG(?:-w?:@1..3@5..28@30..39@43@46..47@49..57@61..62-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-g))(?:UNIT_NAME?:mylib3__Lib3))
 
 Test of an valid invalid module name
   $ FILE=not-a-module-name.ml
   $ printf "(4:File%d:%s)" ${#FILE} $FILE | dune ocaml-merlin | sed -E "s/[[:digit:]]+:/\?:/g"
-  ((?:STDLIB?:/OCAMLC_WHERE)(?:EXCLUDE_QUERY_DIR)(?:B?:$TESTCASE_ROOT/_build/default/.not-a-module-name.eobjs/byte)(?:S?:$TESTCASE_ROOT)(?:FLG(?:-w?:@1..3@5..28@30..39@43@46..47@49..57@61..62-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-w?:-?:-g)))
+  ((?:INDEX?:$TESTCASE_ROOT/_build/default/.not-a-module-name.eobjs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.main.eobjs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.mylib3.objs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.mylib.objs/cctx.ocaml-index)(?:STDLIB?:/OCAMLC_WHERE)(?:SOURCE_ROOT?:$TESTCASE_ROOT)(?:EXCLUDE_QUERY_DIR)(?:B?:$TESTCASE_ROOT/_build/default/.not-a-module-name.eobjs/byte)(?:S?:$TESTCASE_ROOT)(?:FLG(?:-w?:@1..3@5..28@30..39@43@46..47@49..57@61..62-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-w?:-?:-g))(?:UNIT_NAME?:dune__exe__Not-a-module-name))
 
 Dune should also provide configuration when the file is in the build folder
   $ FILE=$PWD/_build/default/lib3.ml
   $ printf "(4:File%d:%s)" ${#FILE} $FILE | dune ocaml-merlin | sed -E "s/[[:digit:]]+:/\?:/g"
-  ((?:STDLIB?:/OCAMLC_WHERE)(?:EXCLUDE_QUERY_DIR)(?:B?:$TESTCASE_ROOT/_build/default/.mylib.objs/byte)(?:B?:$TESTCASE_ROOT/_build/default/.mylib3.objs/byte)(?:S?:$TESTCASE_ROOT)(?:FLG(?:-open?:Mylib3))(?:FLG(?:-w?:@1..3@5..28@30..39@43@46..47@49..57@61..62-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-g)))
+  ((?:INDEX?:$TESTCASE_ROOT/_build/default/.not-a-module-name.eobjs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.main.eobjs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.mylib3.objs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.mylib.objs/cctx.ocaml-index)(?:STDLIB?:/OCAMLC_WHERE)(?:SOURCE_ROOT?:$TESTCASE_ROOT)(?:EXCLUDE_QUERY_DIR)(?:B?:$TESTCASE_ROOT/_build/default/.mylib.objs/byte)(?:B?:$TESTCASE_ROOT/_build/default/.mylib3.objs/byte)(?:S?:$TESTCASE_ROOT)(?:FLG(?:-open?:Mylib3))(?:FLG(?:-w?:@1..3@5..28@30..39@43@46..47@49..57@61..62-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-g))(?:UNIT_NAME?:mylib3__Lib3))
 
   $ FILE=_build/default/lib3.ml
   $ printf "(4:File%d:%s)" ${#FILE} $FILE | dune ocaml-merlin | sed -E "s/[[:digit:]]+:/\?:/g"
-  ((?:STDLIB?:/OCAMLC_WHERE)(?:EXCLUDE_QUERY_DIR)(?:B?:$TESTCASE_ROOT/_build/default/.mylib.objs/byte)(?:B?:$TESTCASE_ROOT/_build/default/.mylib3.objs/byte)(?:S?:$TESTCASE_ROOT)(?:FLG(?:-open?:Mylib3))(?:FLG(?:-w?:@1..3@5..28@30..39@43@46..47@49..57@61..62-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-g)))
+  ((?:INDEX?:$TESTCASE_ROOT/_build/default/.not-a-module-name.eobjs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.main.eobjs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.mylib3.objs/cctx.ocaml-index)(?:INDEX?:$TESTCASE_ROOT/_build/default/.mylib.objs/cctx.ocaml-index)(?:STDLIB?:/OCAMLC_WHERE)(?:SOURCE_ROOT?:$TESTCASE_ROOT)(?:EXCLUDE_QUERY_DIR)(?:B?:$TESTCASE_ROOT/_build/default/.mylib.objs/byte)(?:B?:$TESTCASE_ROOT/_build/default/.mylib3.objs/byte)(?:S?:$TESTCASE_ROOT)(?:FLG(?:-open?:Mylib3))(?:FLG(?:-w?:@1..3@5..28@30..39@43@46..47@49..57@61..62-?:-strict-sequence?:-strict-formats?:-short-paths?:-keep-locs?:-g))(?:UNIT_NAME?:mylib3__Lib3))
diff --git a/test/blackbox-tests/test-cases/merlin/src-dirs-of-deps.t b/test/blackbox-tests/test-cases/merlin/src-dirs-of-deps.t
index 178fccc1c7b..cfe9cf7596f 100644
--- a/test/blackbox-tests/test-cases/merlin/src-dirs-of-deps.t
+++ b/test/blackbox-tests/test-cases/merlin/src-dirs-of-deps.t
@@ -23,7 +23,13 @@ library also has more than one src dir.
   $ dune build lib2/.merlin-conf/lib-lib2
   $ dune ocaml merlin dump-config $PWD/lib2
   Lib2: _build/default/lib2/lib2
-  ((STDLIB /OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/lib1/.lib1.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib2/.lib2.objs/cctx.ocaml-index)
+   (STDLIB /OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/lib1/.lib1.objs/byte)
@@ -42,9 +48,16 @@ library also has more than one src dir.
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME lib2))
   Lib2: _build/default/lib2/lib2.ml-gen
-  ((STDLIB /OPAM_PREFIX)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/lib1/.lib1.objs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/lib2/.lib2.objs/cctx.ocaml-index)
+   (STDLIB /OPAM_PREFIX)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/lib1/.lib1.objs/byte)
@@ -63,4 +76,5 @@ library also has more than one src dir.
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME lib2))
diff --git a/test/blackbox-tests/test-cases/merlin/symlinks.t/run.t b/test/blackbox-tests/test-cases/merlin/symlinks.t/run.t
index eb1036d8902..550ff41a105 100644
--- a/test/blackbox-tests/test-cases/merlin/symlinks.t/run.t
+++ b/test/blackbox-tests/test-cases/merlin/symlinks.t/run.t
@@ -31,4 +31,4 @@ Dune ocaml-merlin also accepts paths relative to the current directory
 
   $ dune ocaml merlin dump-config "." --root=".." | head -n 2
   Foo: _build/default/realsrc/foo
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
diff --git a/test/blackbox-tests/test-cases/merlin/unit-names-merlin-gh1233.t/run.t b/test/blackbox-tests/test-cases/merlin/unit-names-merlin-gh1233.t/run.t
index 0a181e434b2..3cd098a65f8 100644
--- a/test/blackbox-tests/test-cases/merlin/unit-names-merlin-gh1233.t/run.t
+++ b/test/blackbox-tests/test-cases/merlin/unit-names-merlin-gh1233.t/run.t
@@ -6,7 +6,13 @@
 
   $ dune ocaml merlin dump-config $PWD
   Foo: _build/default/foo
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/foo/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.eobjs/byte)
@@ -23,9 +29,16 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME dune__exe__Foo))
   Foo: _build/default/foo.ml
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/foo/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/.foo.eobjs/byte)
@@ -42,11 +55,18 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME dune__exe__Foo))
 
   $ dune ocaml merlin dump-config $PWD/foo
   Bar: _build/default/foo/bar
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/foo/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/foo/.foo.objs/byte)
@@ -60,9 +80,16 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo__Bar))
   Bar: _build/default/foo/bar.ml
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/foo/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/foo/.foo.objs/byte)
@@ -76,9 +103,16 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo__Bar))
   Foo: _build/default/foo/foo
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/foo/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/foo/.foo.objs/byte)
@@ -91,9 +125,16 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo))
   Foo: _build/default/foo/foo.ml-gen
-  ((STDLIB /OCAMLC_WHERE)
+  ((INDEX
+    $TESTCASE_ROOT/_build/default/.foo.eobjs/cctx.ocaml-index)
+   (INDEX
+    $TESTCASE_ROOT/_build/default/foo/.foo.objs/cctx.ocaml-index)
+   (STDLIB /OCAMLC_WHERE)
+   (SOURCE_ROOT
+    $TESTCASE_ROOT)
    (EXCLUDE_QUERY_DIR)
    (B
     $TESTCASE_ROOT/_build/default/foo/.foo.objs/byte)
@@ -106,7 +147,8 @@
      -strict-formats
      -short-paths
      -keep-locs
-     -g)))
+     -g))
+   (UNIT_NAME foo))
 
 FIXME : module Foo is not unbound
 This test is disabled because it depends on root detection and is not reproducible.
diff --git a/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/dune-workspace b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/dune-workspace
new file mode 100644
index 00000000000..1863cf14648
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/dune-workspace
@@ -0,0 +1 @@
+(lang dune 3.5)
diff --git a/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/run.t b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/run.t
new file mode 100644
index 00000000000..0da97dd5b48
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/run.t
@@ -0,0 +1,25 @@
+  $ mkdir bin
+  $ cp $(which ocaml_index) bin/ocaml-index
+  $ export PATH=bin:$PATH
+
+Building from the workspace folder creates all three indexes:
+  $ dune build @ocaml-index
+  $ find . -name '*.ocaml-index' | sort
+  ./_build/default/sub-project/bin/.main.eobjs/cctx.ocaml-index
+  ./_build/default/sub-project/lib/.subprojectlib.objs/cctx.ocaml-index
+  ./_build/default/sub-project2/lib/.subprojectlib2.objs/cctx.ocaml-index
+
+  $ dune clean
+
+Building from one of the sub-projects folder also creates all three indexes:
+  $ cd sub-project 
+  $ export PATH=../bin:$PATH
+  $ dune build --workspace=../dune-workspace --root=.. @sub-project/ocaml-index
+  Entering directory '..'
+  Leaving directory '..'
+  $ cd ..
+
+  $ find . -name '*.ocaml-index' | sort
+  ./_build/default/sub-project/bin/.main.eobjs/cctx.ocaml-index
+  ./_build/default/sub-project/lib/.subprojectlib.objs/cctx.ocaml-index
+  ./_build/default/sub-project2/lib/.subprojectlib2.objs/cctx.ocaml-index
diff --git a/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project/bin/dune b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project/bin/dune
new file mode 100644
index 00000000000..f186fb0b98e
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project/bin/dune
@@ -0,0 +1,4 @@
+(executable
+ (name main)
+ (public_name main)
+ (libraries subprojectlib subprojectlib2))
diff --git a/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project/bin/main.ml b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project/bin/main.ml
new file mode 100644
index 00000000000..f4d83d9b0fa
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project/bin/main.ml
@@ -0,0 +1,2 @@
+print_int Subprojectlib2.subproject_value;
+ print_endline "test"
diff --git a/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project/dune-project b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project/dune-project
new file mode 100644
index 00000000000..ec073f599c7
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project/dune-project
@@ -0,0 +1,2 @@
+(lang dune 3.5)
+
diff --git a/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project/lib/dune b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project/lib/dune
new file mode 100644
index 00000000000..e260b1dbc40
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project/lib/dune
@@ -0,0 +1,3 @@
+(library
+ (name subprojectlib)
+ (public_name subprojectlib))
diff --git a/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project/lib/subprojectlib.ml b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project/lib/subprojectlib.ml
new file mode 100644
index 00000000000..e22b021be33
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project/lib/subprojectlib.ml
@@ -0,0 +1,2 @@
+let subproject_value = 42
+let () = print_int subproject_value
diff --git a/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project/subprojectlib.opam b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project/subprojectlib.opam
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project2/dune-project b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project2/dune-project
new file mode 100644
index 00000000000..ec073f599c7
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project2/dune-project
@@ -0,0 +1,2 @@
+(lang dune 3.5)
+
diff --git a/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project2/lib/dune b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project2/lib/dune
new file mode 100644
index 00000000000..a038335e952
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project2/lib/dune
@@ -0,0 +1,3 @@
+(library
+ (name subprojectlib2)
+ (public_name subprojectlib2))
diff --git a/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project2/lib/subprojectlib2.ml b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project2/lib/subprojectlib2.ml
new file mode 100644
index 00000000000..3f4d7e50ac8
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project2/lib/subprojectlib2.ml
@@ -0,0 +1 @@
+let subproject_value = 42
diff --git a/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project2/subprojectlib2.opam b/test/blackbox-tests/test-cases/ocaml-index/different-workspace-root.t/sub-project2/subprojectlib2.opam
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/test/blackbox-tests/test-cases/ocaml-index/dune b/test/blackbox-tests/test-cases/ocaml-index/dune
new file mode 100644
index 00000000000..756128c6037
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/dune
@@ -0,0 +1,3 @@
+(cram
+ (applies_to :whole_subtree)
+ (deps %{bin:ocaml_index}))
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/dune b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/dune
new file mode 100644
index 00000000000..2baf96810c4
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/dune
@@ -0,0 +1,3 @@
+(executable
+ (name main)
+ (libraries otherlib vendored_lib pmodlib))
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/dune-project b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/dune-project
new file mode 100644
index 00000000000..1614d3d2263
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/dune-project
@@ -0,0 +1,3 @@
+(lang dune 3.5)
+(implicit_transitive_deps false)
+
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/dune-workspace b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/dune-workspace
new file mode 100644
index 00000000000..1863cf14648
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/dune-workspace
@@ -0,0 +1 @@
+(lang dune 3.5)
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/implicit-lib/dune b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/implicit-lib/dune
new file mode 100644
index 00000000000..cdee168bdbe
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/implicit-lib/dune
@@ -0,0 +1,2 @@
+(library
+ (name imp_lib))
\ No newline at end of file
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/implicit-lib/imp_lib.ml b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/implicit-lib/imp_lib.ml
new file mode 100644
index 00000000000..85205179074
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/implicit-lib/imp_lib.ml
@@ -0,0 +1,2 @@
+let imp_x = 42
+type t
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/lib/dune b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/lib/dune
new file mode 100644
index 00000000000..534cbaeb840
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/lib/dune
@@ -0,0 +1,3 @@
+(library
+ (name otherlib)
+ (libraries imp_lib))
\ No newline at end of file
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/lib/otherlib.ml b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/lib/otherlib.ml
new file mode 100644
index 00000000000..80450081d6b
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/lib/otherlib.ml
@@ -0,0 +1,6 @@
+type u = Imp_lib.t
+
+let fromotherlib = 36
+let do_something () = ignore fromotherlib
+
+include Imp_lib
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/lib/otherlib.mli b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/lib/otherlib.mli
new file mode 100644
index 00000000000..68328f9ef80
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/lib/otherlib.mli
@@ -0,0 +1,6 @@
+val do_something : unit -> unit
+val fromotherlib : int
+
+
+include (module type of Imp_lib)
+type u = Imp_lib.t
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/main.ml b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/main.ml
new file mode 100644
index 00000000000..b77bf81a32c
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/main.ml
@@ -0,0 +1,3 @@
+print_int Othermod.(other + Otherlib.fromotherlib + Otherlib.imp_x);;
+print_int Vendored_lib.value;;
+print_int Pmodlib.x;;
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/othermod.ml b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/othermod.ml
new file mode 100644
index 00000000000..64a086316ee
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/othermod.ml
@@ -0,0 +1,2 @@
+let y = 36
+let other = 42 + y
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/private-module/dune b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/private-module/dune
new file mode 100644
index 00000000000..f4ecbe9c95b
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/private-module/dune
@@ -0,0 +1,3 @@
+(library
+ (name pmodlib)
+ (private_modules pmod ))
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/private-module/pmod.ml b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/private-module/pmod.ml
new file mode 100644
index 00000000000..7fecab12d41
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/private-module/pmod.ml
@@ -0,0 +1 @@
+let x = 42
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/private-module/pmodlib.ml b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/private-module/pmodlib.ml
new file mode 100644
index 00000000000..19d782a0500
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/private-module/pmodlib.ml
@@ -0,0 +1 @@
+include Pmod
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/run.t b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/run.t
new file mode 100644
index 00000000000..9f34a834a57
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/run.t
@@ -0,0 +1,39 @@
+  $ mkdir bin
+  $ cp $(which ocaml_index) bin/ocaml-index
+  $ export PATH=bin:$PATH
+
+  $ dune exec ./main.exe
+  1564242
+
+The @check alias does not build indexes:
+(it might at some point if the process becomes fast-enough)
+
+  $ dune build @check
+
+  $ find . -name '*.ocaml-index' | sort
+
+The @ocaml-index indexes the entire workspace, including librairies that might
+not be directly used and thus usually not built by @check:
+
+  $ dune build @ocaml-index
+
+  $ find . -name '*.ocaml-index' | sort
+  ./_build/default/.main.eobjs/cctx.ocaml-index
+  ./_build/default/implicit-lib/.imp_lib.objs/cctx.ocaml-index
+  ./_build/default/lib/.otherlib.objs/cctx.ocaml-index
+  ./_build/default/private-module/.pmodlib.objs/cctx.ocaml-index
+  ./_build/default/sub-project/.subprojectlib.objs/cctx.ocaml-index
+  ./_build/default/vendor/otherproject/.private_lib.objs/cctx.ocaml-index
+  ./_build/default/vendor/otherproject/.vendored_lib.objs/cctx.ocaml-index
+
+
+  $ FILE=$PWD/main.ml
+  $ printf "(4:File%d:%s)" ${#FILE} $FILE | dune ocaml-merlin |
+  > sed -E "s/[[:digit:]]+:/\?:/g" | tr '(' '\n' | grep ":INDEX?"
+  ?:INDEX?:$TESTCASE_ROOT/_build/default/.main.eobjs/cctx.ocaml-index)
+  ?:INDEX?:$TESTCASE_ROOT/_build/default/implicit-lib/.imp_lib.objs/cctx.ocaml-index)
+  ?:INDEX?:$TESTCASE_ROOT/_build/default/lib/.otherlib.objs/cctx.ocaml-index)
+  ?:INDEX?:$TESTCASE_ROOT/_build/default/private-module/.pmodlib.objs/cctx.ocaml-index)
+  ?:INDEX?:$TESTCASE_ROOT/_build/default/sub-project/.subprojectlib.objs/cctx.ocaml-index)
+  ?:INDEX?:$TESTCASE_ROOT/_build/default/vendor/otherproject/.private_lib.objs/cctx.ocaml-index)
+  ?:INDEX?:$TESTCASE_ROOT/_build/default/vendor/otherproject/.vendored_lib.objs/cctx.ocaml-index)
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/sub-project/dune b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/sub-project/dune
new file mode 100644
index 00000000000..e260b1dbc40
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/sub-project/dune
@@ -0,0 +1,3 @@
+(library
+ (name subprojectlib)
+ (public_name subprojectlib))
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/sub-project/dune-project b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/sub-project/dune-project
new file mode 100644
index 00000000000..ec073f599c7
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/sub-project/dune-project
@@ -0,0 +1,2 @@
+(lang dune 3.5)
+
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/sub-project/subprojectlib.ml b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/sub-project/subprojectlib.ml
new file mode 100644
index 00000000000..e22b021be33
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/sub-project/subprojectlib.ml
@@ -0,0 +1,2 @@
+let subproject_value = 42
+let () = print_int subproject_value
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/sub-project/subprojectlib.opam b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/sub-project/subprojectlib.opam
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/vendor/dune b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/vendor/dune
new file mode 100644
index 00000000000..806de809491
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/vendor/dune
@@ -0,0 +1 @@
+(vendored_dirs *)
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/vendor/otherproject/dune b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/vendor/otherproject/dune
new file mode 100644
index 00000000000..1edde22bcc6
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/vendor/otherproject/dune
@@ -0,0 +1,8 @@
+(library
+ (name vendored_lib)
+ (public_name vendored_lib)
+ (modules vendored_lib))
+
+(library
+ (name private_lib) ; This private lib is not built when vendored
+ (modules private_lib))
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/vendor/otherproject/dune-project b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/vendor/otherproject/dune-project
new file mode 100644
index 00000000000..929c696e561
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/vendor/otherproject/dune-project
@@ -0,0 +1 @@
+(lang dune 2.0)
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/vendor/otherproject/private_lib.ml b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/vendor/otherproject/private_lib.ml
new file mode 100644
index 00000000000..2edb08b94b0
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/vendor/otherproject/private_lib.ml
@@ -0,0 +1 @@
+let more = "less"
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/vendor/otherproject/vendored_lib.ml b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/vendor/otherproject/vendored_lib.ml
new file mode 100644
index 00000000000..e51d91c9bc2
--- /dev/null
+++ b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/vendor/otherproject/vendored_lib.ml
@@ -0,0 +1 @@
+let value = 42
diff --git a/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/vendor/otherproject/vendored_lib.opam b/test/blackbox-tests/test-cases/ocaml-index/project-indexation.t/vendor/otherproject/vendored_lib.opam
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/test/blackbox-tests/utils/dune b/test/blackbox-tests/utils/dune
index 5755469a546..3d1072f7bf0 100644
--- a/test/blackbox-tests/utils/dune
+++ b/test/blackbox-tests/utils/dune
@@ -33,3 +33,8 @@
  (name sherlodoc)
  (modules sherlodoc)
  (libraries stdune))
+
+(executable
+ (modules ocaml_index)
+ (name ocaml_index)
+ (libraries cmdliner))
diff --git a/test/blackbox-tests/utils/ocaml_index.ml b/test/blackbox-tests/utils/ocaml_index.ml
new file mode 100644
index 00000000000..1c4507dc24d
--- /dev/null
+++ b/test/blackbox-tests/utils/ocaml_index.ml
@@ -0,0 +1,101 @@
+(** Mock ocaml-index real CLI *)
+
+open Cmdliner
+
+let touch file =
+  let chan = open_out file in
+  close_out chan
+;;
+
+module Common = struct
+  let set_log_level _ _ = ()
+
+  let verbose =
+    let doc = "increase log verbosity" in
+    Arg.(value & flag & info [ "v"; "verbose" ] ~doc)
+  ;;
+
+  let debug =
+    let doc = "set maximum log verbosity" in
+    Arg.(value & flag & info [ "debug" ] ~doc)
+  ;;
+
+  let with_log = Term.(const set_log_level $ debug $ verbose)
+
+  let output_file =
+    let doc = "name of the generated index" in
+    Arg.(value & opt string "project.ocaml-index" & info [ "o"; "output-file" ] ~doc)
+  ;;
+end
+
+module Aggregate = struct
+  let from_files _ _ output_file _ _ () = touch output_file
+
+  let root =
+    let doc = "if provided all locations will be appended to that path" in
+    Arg.(value & opt (some string) None & info [ "root" ] ~doc)
+  ;;
+
+  let files =
+    let doc = "the files to index" in
+    Arg.(value & pos_all string [] & info [] ~doc)
+  ;;
+
+  let build_path =
+    let doc = "an extra directory to add to the load path" in
+    Arg.(value & opt_all string [] & info [ "I" ] ~doc)
+  ;;
+
+  let store_shapes =
+    let doc = "aggregate input-indexes shapes and store them in the new index" in
+    Arg.(value & flag & info [ "store-shapes" ] ~doc)
+  ;;
+
+  let term =
+    Term.(
+      const from_files
+      $ store_shapes
+      $ root
+      $ Common.output_file
+      $ build_path
+      $ files
+      $ Common.with_log)
+  ;;
+
+  let cmd =
+    let info =
+      let doc = "builds the index for a single $(i, .cmt) file" in
+      Cmd.info "aggregate" ~doc
+    in
+    Cmd.v info term
+  ;;
+end
+
+module Dump = struct
+  let dump file () = Printf.printf "Dump %s" file
+
+  let file =
+    let doc = "the file to dump" in
+    Arg.(required & pos 0 (some string) None & info [] ~doc)
+  ;;
+
+  let term = Term.(const dump $ file $ Common.with_log)
+
+  let cmd =
+    let info =
+      let doc = "print the content of an index file to stdout" in
+      Cmd.info "dump" ~doc
+    in
+    Cmd.v info term
+  ;;
+end
+
+let subcommands =
+  let info =
+    let doc = "An indexer for OCaml's artifacts" in
+    Cmd.info "ocaml-index" ~doc
+  in
+  Cmd.group info ~default:Aggregate.term [ Aggregate.cmd; Dump.cmd ]
+;;
+
+let () = exit (Cmd.eval subcommands)
diff --git a/test/expect-tests/persistent_tests.ml b/test/expect-tests/persistent_tests.ml
index 96263336a2a..47b6fed45c7 100644
--- a/test/expect-tests/persistent_tests.ml
+++ b/test/expect-tests/persistent_tests.ml
@@ -43,8 +43,8 @@ let%expect_test "persistent digests" =
     7e311b06ebde9ff1708e4c3a1d3f5633
     ---
 
-    merlin-conf version 4
-    782b1c9ea57a40a427f80fa24ba6d853
+    merlin-conf version 5
+    49e3a1010b7218f5b229d98991d6d11d
     ---
 
     INCREMENTAL-DB version 5