diff --git a/compiler/catala_utils/cli.ml b/compiler/catala_utils/cli.ml
index f975bc2b..3c88b006 100644
--- a/compiler/catala_utils/cli.ml
+++ b/compiler/catala_utils/cli.ml
@@ -39,7 +39,6 @@ type options = {
   mutable message_format : message_format_enum;
   mutable trace : bool;
   mutable plugins_dirs : string list;
-  mutable build_dir : string option;
   mutable disable_warnings : bool;
   mutable max_prec_digits : int;
 }
@@ -58,7 +57,6 @@ let globals =
     message_format = Human;
     trace = false;
     plugins_dirs = [];
-    build_dir = None;
     disable_warnings = false;
     max_prec_digits = 20;
   }
@@ -71,7 +69,6 @@ let enforce_globals
     ?message_format
     ?trace
     ?plugins_dirs
-    ?build_dir
     ?disable_warnings
     ?max_prec_digits
     () =
@@ -82,7 +79,6 @@ let enforce_globals
   Option.iter (fun x -> globals.message_format <- x) message_format;
   Option.iter (fun x -> globals.trace <- x) trace;
   Option.iter (fun x -> globals.plugins_dirs <- x) plugins_dirs;
-  Option.iter (fun x -> globals.build_dir <- x) build_dir;
   Option.iter (fun x -> globals.disable_warnings <- x) disable_warnings;
   Option.iter (fun x -> globals.max_prec_digits <- x) max_prec_digits;
   globals
@@ -112,7 +108,7 @@ module Flags = struct
               | _ -> assert false )
       in
       required
-      & pos 0 (some converter) None
+      & pos ~rev:true 0 (some converter) None
       & Arg.info [] ~docv:"FILE" ~docs:Manpage.s_arguments
           ~doc:"Catala master file to be compiled."
 
@@ -191,15 +187,6 @@ module Flags = struct
       in
       value & opt_all string default & info ["plugin-dir"] ~docv:"DIR" ~env ~doc
 
-    let build_dir =
-      value
-      & opt (some string) None
-      & info ["build-dir"] ~docv:"DIR"
-          ~doc:
-            "Directory where build artefacts are expected to be found. This \
-             doesn't affect outptuts, but is used when looking up compiled \
-             modules."
-
     let disable_warnings =
       value
       & flag
@@ -223,14 +210,13 @@ module Flags = struct
           message_format
           trace
           plugins_dirs
-          build_dir
           disable_warnings
           max_prec_digits : options =
         if debug then Printexc.record_backtrace true;
         (* This sets some global refs for convenience, but most importantly
            returns the options record. *)
         enforce_globals ~language ~debug ~color ~message_format ~trace
-          ~plugins_dirs ~build_dir ~disable_warnings ~max_prec_digits ()
+          ~plugins_dirs ~disable_warnings ~max_prec_digits ()
       in
       Term.(
         const make
@@ -240,7 +226,6 @@ module Flags = struct
         $ message_format
         $ trace
         $ plugins_dirs
-        $ build_dir
         $ disable_warnings
         $ max_prec_digits)
 
@@ -253,6 +238,13 @@ module Flags = struct
       Term.(const make $ input_file $ flags)
   end
 
+  let include_dirs =
+    value
+    & opt_all string []
+    & info ["I";"include"] ~docv:"DIR"
+      ~doc:
+        "Include directory to lookup for compiled module files."
+
   let check_invariants =
     value
     & flag
@@ -314,17 +306,6 @@ module Flags = struct
           "Performs closure conversion on the lambda calculus. Implies \
            $(b,--avoid-exceptions) and $(b,--optimize)."
 
-  let link_modules =
-    value
-    & opt_all file []
-    & info ["use"; "u"] ~docv:"FILE"
-        ~doc:
-          "Specifies an additional module to be linked to the Catala program. \
-           $(i,FILE) must be a catala file with a metadata section expressing \
-           what is exported ; for interpretation, a compiled OCaml shared \
-           module by the same basename (either .cmo or .cmxs) will be \
-           expected."
-
   let disable_counterexamples =
     value
     & flag
@@ -334,6 +315,14 @@ module Flags = struct
           "Disables the search for counterexamples. Useful when you want a \
            deterministic output from the Catala compiler, since provers can \
            have some randomness in them."
+
+  let build_dirs =
+    value
+    & opt_all string ["."; "_build"]
+    & info ["build-dir"] ~docv:"DIR"
+      ~env:(Cmd.Env.info "CATALA_BUILD_DIR")
+      ~doc:
+        "Directory where compiled modules are expected to be found (this option does not affect catala outputs)"
 end
 
 (* Retrieve current version from dune *)
diff --git a/compiler/catala_utils/cli.mli b/compiler/catala_utils/cli.mli
index 4aca040d..61fd688f 100644
--- a/compiler/catala_utils/cli.mli
+++ b/compiler/catala_utils/cli.mli
@@ -43,7 +43,6 @@ type options = private {
   mutable message_format : message_format_enum;
   mutable trace : bool;
   mutable plugins_dirs : string list;
-  mutable build_dir : string option;
   mutable disable_warnings : bool;
   mutable max_prec_digits : int;
 }
@@ -63,7 +62,6 @@ val enforce_globals :
   ?message_format:message_format_enum ->
   ?trace:bool ->
   ?plugins_dirs:string list ->
-  ?build_dir:string option ->
   ?disable_warnings:bool ->
   ?max_prec_digits:int ->
   unit ->
@@ -101,8 +99,9 @@ module Flags : sig
   val optimize : bool Term.t
   val avoid_exceptions : bool Term.t
   val closure_conversion : bool Term.t
-  val link_modules : string list Term.t
+  val include_dirs : string list Term.t
   val disable_counterexamples : bool Term.t
+  val build_dirs : string list Term.t
 end
 
 (** {2 Command-line application} *)
diff --git a/compiler/catala_utils/file.ml b/compiler/catala_utils/file.ml
index 6566ad46..5839f21a 100644
--- a/compiler/catala_utils/file.ml
+++ b/compiler/catala_utils/file.ml
@@ -117,12 +117,27 @@ let check_directory d =
     if Sys.is_directory d then Some d else None
   with Unix.Unix_error _ | Sys_error _ -> None
 
-let ( / ) = Filename.concat
+let check_file f =
+  try if Sys.is_directory f then None else Some f
+  with Unix.Unix_error _ | Sys_error _ -> None
+
+let ( / ) a b =
+  if a = "" || a = Filename.current_dir_name then b
+  else Filename.concat a b
 let dirname = Filename.dirname
 let ( /../ ) a b = dirname a / b
 let ( -.- ) file ext = Filename.chop_extension file ^ "." ^ ext
-let equal = String.equal
-let compare = String.compare
+
+let path_to_list path =
+  String.split_on_char Filename.dir_sep.[0] path
+  |> List.filter (fun d -> d <> "")
+
+let equal a b =
+  String.equal (String.lowercase_ascii a) (String.lowercase_ascii b)
+
+let compare a b =
+  String.compare (String.lowercase_ascii a) (String.lowercase_ascii b)
+
 let format ppf t = Format.fprintf ppf "\"@{<cyan>%s@}\"" t
 
 module Set = Set.Make (struct
@@ -131,6 +146,13 @@ module Set = Set.Make (struct
   let compare = compare
 end)
 
+module Map = Map.Make (struct
+  type nonrec t = t
+
+  let compare = compare
+  let format = format
+end)
+
 let scan_tree f t =
   let is_dir t =
     try Sys.is_directory t
@@ -143,7 +165,7 @@ let scan_tree f t =
     Sys.readdir d
     |> Array.to_list
     |> List.filter not_hidden
-    |> (if d = "." then fun t -> t else List.map (fun t -> d / t))
+    |> List.map (fun t -> d / t)
     |> do_files
   and do_files flist =
     let dirs, files =
@@ -154,3 +176,42 @@ let scan_tree f t =
       (Seq.filter_map f (List.to_seq files))
   in
   do_files [t]
+
+module Tree = struct
+  type path = t
+
+  type item = F | D of t
+  and t = (path * item) Map.t Lazy.t
+
+  let empty = lazy Map.empty
+
+  let rec build path = lazy
+    (Array.fold_left
+       (fun m f ->
+          let path = path / f in
+          match Sys.is_directory path with
+          | true -> Map.add f (path, D (build path)) m
+          | false -> Map.add f (path, F) m
+          | exception Sys_error _ -> m)
+       Map.empty
+       (Sys.readdir path))
+
+  let subtree t path =
+    let rec aux t = function
+      | [] -> t
+      | dir :: path ->
+        match Map.find_opt dir (Lazy.force t) with
+        | Some (_, D sub) -> aux sub path
+        | Some (_, F) | None -> raise Not_found
+    in
+    aux t (path_to_list path)
+
+  let lookup t path =
+    try
+      let t = subtree t (dirname path) in
+      match Map.find_opt (Filename.basename path) (Lazy.force t) with
+      | Some (path, F) -> Some path
+      | Some (_, D _) | None -> None
+    with Not_found -> None
+
+end
diff --git a/compiler/catala_utils/file.mli b/compiler/catala_utils/file.mli
index 644d06d0..f2025607 100644
--- a/compiler/catala_utils/file.mli
+++ b/compiler/catala_utils/file.mli
@@ -85,9 +85,12 @@ val check_directory : t -> t option
 (** Checks if the given directory exists and returns it normalised (as per
     [Unix.realpath]). *)
 
+val check_file : t -> t option
+(** Returns its argument if it exists and is a plain file, [None] otherwise. Does not do resolution like [check_directory]. *)
+
 val ( / ) : t -> t -> t
 (** [Filename.concat]: Sugar to allow writing
-    [File.("some" / "relative" / "path")] *)
+    [File.("some" / "relative" / "path")]. As an exception, if the lhs is [.], returns the rhs unchanged. *)
 
 val dirname : t -> t
 (** [Filename.dirname], re-exported for convenience *)
@@ -100,18 +103,42 @@ val ( -.- ) : t -> string -> t
     with the given one (which shouldn't contain a dot) *)
 
 val equal : t -> t -> bool
-(** String comparison no fancy file resolution *)
+(** Case-insensitive string comparison (no file resolution whatsoever) *)
 
 val compare : t -> t -> int
-(** String comparison no fancy file resolution *)
+(** Case-insensitive string comparison (no file resolution whatsoever) *)
 
 val format : Format.formatter -> t -> unit
 (** Formats a filename in a consistent style, with double-quotes and color (when
     the output supports) *)
 
 module Set : Set.S with type elt = t
+module Map : Map.S with type key = t
 
 val scan_tree : (t -> 'a option) -> t -> 'a Seq.t
 (** Recursively scans a directory for files. Directories or files matching ".*"
     or "_*" are ignored. Unreadable files or subdirectories are ignored with a
     debug message. If [t] is a plain file, scan just that non-recursively. *)
+
+module Tree: sig
+  (** A lazy tree structure mirroring the filesystem ; uses the comparison from File, so paths are case-insensitive. *)
+
+  type path = t (** Alias for [File.t] *)
+
+  type item =
+    | F (** Plain file *)
+    | D of t (** Directory with subtree *)
+  and t = (path * item) Map.t Lazy.t
+  (** Contents of a directory, lazily loaded. The map keys are the basenames of the files and subdirectories, while the values contain the original path (with correct capitalisation) *)
+
+  val empty: t
+
+  val build: path -> t
+  (** Lazily builds a [Tree.path] from the files read at [path]. The names in the maps are qualified (i.e. they all start with ["path/"]) *)
+
+  val subtree: t -> path -> t
+  (** Looks up a path within a lazy tree *)
+
+  val lookup: t -> path -> path option
+  (** Checks if there is a matching plain file (case-insensitively) ; and returns its path with the correct case if so *)
+end
diff --git a/compiler/catala_web_interpreter.ml b/compiler/catala_web_interpreter.ml
index baf74bc9..c22dc6a1 100644
--- a/compiler/catala_web_interpreter.ml
+++ b/compiler/catala_web_interpreter.ml
@@ -23,7 +23,7 @@ let () =
              ~language:(Some language) ~debug:false ~color:Never ~trace ()
          in
          let prg, ctx, _type_order =
-           Passes.dcalc options ~link_modules:[] ~optimize:false
+           Passes.dcalc options ~includes:File.Tree.empty ~optimize:false
              ~check_invariants:false
          in
          Shared_ast.Interpreter.interpret_program_dcalc prg
diff --git a/compiler/desugared/from_surface.ml b/compiler/desugared/from_surface.ml
index 38c4faaf..2b57d2b5 100644
--- a/compiler/desugared/from_surface.ml
+++ b/compiler/desugared/from_surface.ml
@@ -1527,7 +1527,16 @@ let translate_program (ctxt : Name_resolution.context) (surface : S.program) :
         (fun prgm child -> process_structure prgm child)
         prgm children
     | S.CodeBlock (block, _, _) -> process_code_block ctxt prgm block
-    | S.LawInclude _ | S.LawText _ | S.ModuleUse _ | S.ModuleDef _ -> prgm
+    | S.ModuleDef ((name, pos) as mname) ->
+      let file = Filename.basename (Pos.get_file pos) in
+      if not File.(equal name (Filename.remove_extension file))
+      then
+        Message.raise_spanned_error pos
+          "Module declared as %a, which does not match the file name %a"
+          ModuleName.format (ModuleName.of_string mname)
+          File.format file
+      else prgm
+    | S.LawInclude _ | S.LawText _ | S.ModuleUse _ -> prgm
   in
   let desugared =
     List.fold_left
diff --git a/compiler/driver.ml b/compiler/driver.ml
index 3da8d9e7..1075c763 100644
--- a/compiler/driver.ml
+++ b/compiler/driver.ml
@@ -42,63 +42,68 @@ let get_lang options file =
          @{<yellow>%s@}, and @{<bold>--language@} was not specified"
         filename)
 
-let load_module_interfaces options program files =
-  let module MS = ModuleName.Set in
-  let to_set intf_list =
-    MS.of_list
-      (List.map (fun (mname, _) -> ModuleName.of_string mname) intf_list)
+let load_module_interfaces includes program =
+  (* Recurse into program modules, looking up files in [using] and loading them *)
+  let err_req_pos chain =
+    List.map (fun m -> Some "Module required from", ModuleName.pos m) chain
+  in
+  let find_module req_chain m =
+    let fname_base = ModuleName.to_string m in
+    let required_from_file = Pos.get_file (ModuleName.pos m) in
+    match
+      Option.to_list (File.check_file File.(required_from_file /../ fname_base)) @
+      List.filter_map
+        (fun (ext, _) ->
+           File.Tree.lookup includes (fname_base ^ ext))
+        extensions
+    with
+    | [] ->
+      Message.raise_multispanned_error (err_req_pos (m::req_chain))
+        "Required module not found: %a"
+        ModuleName.format m
+    | [f] ->
+      f
+    | ms ->
+      Message.raise_multispanned_error
+        (err_req_pos (m::req_chain))
+        "Required module %a matches multiple files: %a"
+        ModuleName.format m
+        (Format.pp_print_list ~pp_sep:Format.pp_print_space File.format)
+        ms
   in
-  let used_modules = to_set program.Surface.Ast.program_modules in
   let load_file f =
-    let lang = get_lang options (FileName f) in
+    let lang =
+      List.assoc
+        (List.assoc (Filename.extension f) extensions)
+        Cli.languages
+    in
     let (mname, intf), using =
-      Surface.Parser_driver.load_interface (FileName f) lang
+      Surface.Parser_driver.load_interface (Cli.FileName f) lang
     in
     (ModuleName.of_string mname, intf), using
   in
-  let module_interfaces = List.map load_file files in
-  let rec check (required, acc) interfaces =
-    let required, acc, remaining =
-      List.fold_left
-        (fun (required, acc, skipped) (((modname, intf), using) as modl) ->
-          if MS.mem modname required then
-            let required =
-              List.fold_left
-                (fun req m -> MS.add (ModuleName.of_string m) req)
-                required using
-            in
-            required, ((modname :> string Mark.pos), intf) :: acc, skipped
-          else required, acc, modl :: skipped)
-        (required, acc, []) interfaces
-    in
-    if List.length remaining < List.length interfaces then
-      (* Loop until fixpoint *)
-      check (required, acc) remaining
-    else required, acc, remaining
+  let rec aux req_chain acc modules =
+    List.fold_left (fun acc mname ->
+        let m = ModuleName.of_string mname in
+        if List.mem_assoc m acc then acc else
+          let f = find_module req_chain m in
+          let (m', intf), using = load_file f in
+          if not (ModuleName.equal m m') then
+            Message.raise_multispanned_error
+              ((Some "Module name declaration", ModuleName.pos m') ::
+               err_req_pos (m::req_chain))
+              "Mismatching module name declaration:";
+          let acc = (m', intf) :: acc in
+          aux (m::req_chain) acc using
+      )
+      acc modules
   in
-  let required, loaded, unused = check (used_modules, []) module_interfaces in
-  let missing =
-    MS.diff required
-      (MS.of_list (List.map (fun (m, _) -> ModuleName.of_string m) loaded))
+  let program_modules =
+    aux [] [] (List.map fst program.Surface.Ast.program_modules)
+    |> List.map (fun (m, i) -> (m : ModuleName.t :> string Mark.pos), i)
   in
-  if (not (MS.is_empty missing)) || unused <> [] then
-    Message.raise_multispanned_error
-      (List.map
-         (fun m ->
-           ( Some
-               (Format.asprintf "Required module not found: %a"
-                  ModuleName.format m),
-             ModuleName.pos m ))
-         (ModuleName.Set.elements missing)
-      @ List.map
-          (fun ((m, _), _) ->
-            ( Some
-                (Format.asprintf "No use was found for this module: %a"
-                   ModuleName.format m),
-              ModuleName.pos m ))
-          unused)
-      "Modules used from the program don't match the command-line";
-  loaded
+  { program with
+    Surface.Ast.program_modules }
 
 module Passes = struct
   (* Each pass takes only its cli options, then calls upon its dependent passes
@@ -108,19 +113,19 @@ module Passes = struct
     Message.emit_debug "@{<bold;magenta>=@} @{<bold>%s@} @{<bold;magenta>=@}"
       (String.uppercase_ascii s)
 
-  let surface options ~link_modules : Surface.Ast.program * Cli.backend_lang =
+  let surface options ~includes : Surface.Ast.program * Cli.backend_lang =
     debug_pass_name "surface";
     let language = get_lang options options.input_file in
     let prg =
       Surface.Parser_driver.parse_top_level_file options.input_file language
     in
     let prg = Surface.Fill_positions.fill_pos_with_legislative_info prg in
-    let program_modules = load_module_interfaces options prg link_modules in
-    { prg with program_modules }, language
+    let prg = load_module_interfaces includes prg in
+    prg, language
 
-  let desugared options ~link_modules :
+  let desugared options ~includes :
       Desugared.Ast.program * Desugared.Name_resolution.context =
-    let prg, _ = surface options ~link_modules in
+    let prg, _ = surface options ~includes in
     debug_pass_name "desugared";
     Message.emit_debug "Name resolution...";
     let ctx = Desugared.Name_resolution.form_context prg in
@@ -138,12 +143,12 @@ module Passes = struct
      uids from strings. Maybe a reduced form should be included directly in
      [prg] for that purpose *)
 
-  let scopelang options ~link_modules :
+  let scopelang options ~includes :
       untyped Scopelang.Ast.program
       * Desugared.Name_resolution.context
       * Desugared.Dependency.ExceptionsDependencies.t
         Desugared.Ast.ScopeDef.Map.t =
-    let prg, ctx = desugared options ~link_modules in
+    let prg, ctx = desugared options ~includes in
     debug_pass_name "scopelang";
     let exceptions_graphs =
       Scopelang.From_desugared.build_exceptions_graph prg
@@ -153,11 +158,11 @@ module Passes = struct
     in
     prg, ctx, exceptions_graphs
 
-  let dcalc options ~link_modules ~optimize ~check_invariants :
+  let dcalc options ~includes ~optimize ~check_invariants :
       typed Dcalc.Ast.program
       * Desugared.Name_resolution.context
       * Scopelang.Dependency.TVertex.t list =
-    let prg, ctx, _ = scopelang options ~link_modules in
+    let prg, ctx, _ = scopelang options ~includes in
     debug_pass_name "dcalc";
     let type_ordering =
       Scopelang.Dependency.check_type_cycles prg.program_ctx.ctx_structs
@@ -193,7 +198,7 @@ module Passes = struct
 
   let lcalc
       options
-      ~link_modules
+      ~includes
       ~optimize
       ~check_invariants
       ~avoid_exceptions
@@ -202,7 +207,7 @@ module Passes = struct
       * Desugared.Name_resolution.context
       * Scopelang.Dependency.TVertex.t list =
     let prg, ctx, type_ordering =
-      dcalc options ~link_modules ~optimize ~check_invariants
+      dcalc options ~includes ~optimize ~check_invariants
     in
     debug_pass_name "lcalc";
     let avoid_exceptions = avoid_exceptions || closure_conversion in
@@ -243,7 +248,7 @@ module Passes = struct
 
   let scalc
       options
-      ~link_modules
+      ~includes
       ~optimize
       ~check_invariants
       ~avoid_exceptions
@@ -252,7 +257,7 @@ module Passes = struct
       * Desugared.Name_resolution.context
       * Scopelang.Dependency.TVertex.t list =
     let prg, ctx, type_ordering =
-      lcalc options ~link_modules ~optimize ~check_invariants ~avoid_exceptions
+      lcalc options ~includes ~optimize ~check_invariants ~avoid_exceptions
         ~closure_conversion
     in
     debug_pass_name "scalc";
@@ -353,6 +358,14 @@ module Commands = struct
                   second_part first_part ScopeName.format scope_uid)
             second_part )
 
+  let include_flags =
+    let mk dirs =
+      lazy (dirs
+            |> List.map (fun d -> Lazy.force (File.Tree.build d))
+            |> List.fold_left (File.Map.union (fun _ x _ -> Some x)) File.Map.empty)
+    in
+    Term.(const mk $ Cli.Flags.include_dirs)
+
   let get_output ?ext options output_file =
     File.get_out_channel ~source_file:options.Cli.input_file ~output_file ?ext
       ()
@@ -362,7 +375,7 @@ module Commands = struct
       ~output_file ?ext ()
 
   let makefile options output =
-    let prg, _ = Passes.surface options ~link_modules:[] in
+    let prg, _ = Passes.surface options ~includes:File.Tree.empty in
     let backend_extensions_list = [".tex"] in
     let source_file =
       match options.Cli.input_file with
@@ -393,7 +406,7 @@ module Commands = struct
       Term.(const makefile $ Cli.Flags.Global.options $ Cli.Flags.output)
 
   let html options output print_only_law wrap_weaved_output =
-    let prg, language = Passes.surface options ~link_modules:[] in
+    let prg, language = Passes.surface options ~includes:File.Tree.empty in
     Message.emit_debug "Weaving literate program into HTML";
     let output_file, with_output =
       get_output_format options ~ext:".html" output
@@ -421,7 +434,7 @@ module Commands = struct
         $ Cli.Flags.wrap_weaved_output)
 
   let latex options output print_only_law wrap_weaved_output =
-    let prg, language = Passes.surface options ~link_modules:[] in
+    let prg, language = Passes.surface options ~includes:File.Tree.empty in
     Message.emit_debug "Weaving literate program into LaTeX";
     let output_file, with_output =
       get_output_format options ~ext:".tex" output
@@ -448,8 +461,8 @@ module Commands = struct
         $ Cli.Flags.print_only_law
         $ Cli.Flags.wrap_weaved_output)
 
-  let exceptions options link_modules ex_scope ex_variable =
-    let _, ctxt, exceptions_graphs = Passes.scopelang options ~link_modules in
+  let exceptions options includes ex_scope ex_variable =
+    let _, ctxt, exceptions_graphs = Passes.scopelang options ~includes in
     let scope_uid = get_scope_uid ctxt ex_scope in
     let variable_uid = get_variable_uid ctxt scope_uid ex_variable in
     Desugared.Print.print_exceptions_graph scope_uid variable_uid
@@ -467,12 +480,12 @@ module Commands = struct
       Term.(
         const exceptions
         $ Cli.Flags.Global.options
-        $ Cli.Flags.link_modules
+        $ include_flags
         $ Cli.Flags.ex_scope
         $ Cli.Flags.ex_variable)
 
-  let scopelang options link_modules output ex_scope_opt =
-    let prg, ctx, _ = Passes.scopelang options ~link_modules in
+  let scopelang options includes output ex_scope_opt =
+    let prg, ctx, _ = Passes.scopelang options ~includes in
     let _output_file, with_output = get_output_format options output in
     with_output
     @@ fun fmt ->
@@ -496,12 +509,12 @@ module Commands = struct
       Term.(
         const scopelang
         $ Cli.Flags.Global.options
-        $ Cli.Flags.link_modules
+        $ include_flags
         $ Cli.Flags.output
         $ Cli.Flags.ex_scope_opt)
 
-  let typecheck options link_modules =
-    let prg, _, _ = Passes.scopelang options ~link_modules in
+  let typecheck options includes =
+    let prg, _, _ = Passes.scopelang options ~includes in
     Message.emit_debug "Typechecking...";
     let _type_ordering =
       Scopelang.Dependency.check_type_cycles prg.program_ctx.ctx_structs
@@ -519,11 +532,11 @@ module Commands = struct
     Cmd.v
       (Cmd.info "typecheck"
          ~doc:"Parses and typechecks a Catala program, without interpreting it.")
-      Term.(const typecheck $ Cli.Flags.Global.options $ Cli.Flags.link_modules)
+      Term.(const typecheck $ Cli.Flags.Global.options $ include_flags)
 
-  let dcalc options link_modules output optimize ex_scope_opt check_invariants =
+  let dcalc options includes output optimize ex_scope_opt check_invariants =
     let prg, ctx, _ =
-      Passes.dcalc options ~link_modules ~optimize ~check_invariants
+      Passes.dcalc options ~includes ~optimize ~check_invariants
     in
     let _output_file, with_output = get_output_format options output in
     with_output
@@ -560,7 +573,7 @@ module Commands = struct
       Term.(
         const dcalc
         $ Cli.Flags.Global.options
-        $ Cli.Flags.link_modules
+        $ include_flags
         $ Cli.Flags.output
         $ Cli.Flags.optimize
         $ Cli.Flags.ex_scope_opt
@@ -568,13 +581,13 @@ module Commands = struct
 
   let proof
       options
-      link_modules
+      includes
       optimize
       ex_scope_opt
       check_invariants
       disable_counterexamples =
     let prg, ctx, _ =
-      Passes.dcalc options ~link_modules ~optimize ~check_invariants
+      Passes.dcalc options ~includes ~optimize ~check_invariants
     in
     Verification.Globals.setup ~optimize ~disable_counterexamples;
     let vcs =
@@ -592,7 +605,7 @@ module Commands = struct
       Term.(
         const proof
         $ Cli.Flags.Global.options
-        $ Cli.Flags.link_modules
+        $ include_flags
         $ Cli.Flags.optimize
         $ Cli.Flags.ex_scope_opt
         $ Cli.Flags.check_invariants
@@ -621,11 +634,11 @@ module Commands = struct
           result)
       results
 
-  let interpret_dcalc options link_modules optimize check_invariants ex_scope =
+  let interpret_dcalc options includes optimize check_invariants build_dirs ex_scope =
     let prg, ctx, _ =
-      Passes.dcalc options ~link_modules ~optimize ~check_invariants
+      Passes.dcalc options ~includes ~optimize ~check_invariants
     in
-    Interpreter.load_runtime_modules prg;
+    Interpreter.load_runtime_modules ~build_dirs prg;
     print_interpretation_results options Interpreter.interpret_program_dcalc prg
       (get_scope_uid ctx ex_scope)
 
@@ -639,14 +652,15 @@ module Commands = struct
       Term.(
         const interpret_dcalc
         $ Cli.Flags.Global.options
-        $ Cli.Flags.link_modules
+        $ include_flags
         $ Cli.Flags.optimize
         $ Cli.Flags.check_invariants
+        $ Cli.Flags.build_dirs
         $ Cli.Flags.ex_scope)
 
   let lcalc
       options
-      link_modules
+      includes
       output
       optimize
       check_invariants
@@ -654,7 +668,7 @@ module Commands = struct
       closure_conversion
       ex_scope_opt =
     let prg, ctx, _ =
-      Passes.lcalc options ~link_modules ~optimize ~check_invariants
+      Passes.lcalc options ~includes ~optimize ~check_invariants
         ~avoid_exceptions ~closure_conversion
     in
     let _output_file, with_output = get_output_format options output in
@@ -680,7 +694,7 @@ module Commands = struct
       Term.(
         const lcalc
         $ Cli.Flags.Global.options
-        $ Cli.Flags.link_modules
+        $ include_flags
         $ Cli.Flags.output
         $ Cli.Flags.optimize
         $ Cli.Flags.check_invariants
@@ -690,16 +704,18 @@ module Commands = struct
 
   let interpret_lcalc
       options
-      link_modules
+      includes
       optimize
       check_invariants
       avoid_exceptions
       closure_conversion
+      build_dirs
       ex_scope =
     let prg, ctx, _ =
-      Passes.lcalc options ~link_modules ~optimize ~check_invariants
+      Passes.lcalc options ~includes ~optimize ~check_invariants
         ~avoid_exceptions ~closure_conversion
     in
+    Interpreter.load_runtime_modules ~build_dirs prg;
     print_interpretation_results options Interpreter.interpret_program_lcalc prg
       (get_scope_uid ctx ex_scope)
 
@@ -713,23 +729,24 @@ module Commands = struct
       Term.(
         const interpret_lcalc
         $ Cli.Flags.Global.options
-        $ Cli.Flags.link_modules
+        $ include_flags
         $ Cli.Flags.optimize
         $ Cli.Flags.check_invariants
         $ Cli.Flags.avoid_exceptions
         $ Cli.Flags.closure_conversion
+        $ Cli.Flags.build_dirs
         $ Cli.Flags.ex_scope)
 
   let ocaml
       options
-      link_modules
+      includes
       output
       optimize
       check_invariants
       avoid_exceptions
       closure_conversion =
     let prg, _, type_ordering =
-      Passes.lcalc options ~link_modules ~optimize ~check_invariants
+      Passes.lcalc options ~includes ~optimize ~check_invariants
         ~avoid_exceptions ~closure_conversion
     in
     let output_file, with_output =
@@ -749,7 +766,7 @@ module Commands = struct
       Term.(
         const ocaml
         $ Cli.Flags.Global.options
-        $ Cli.Flags.link_modules
+        $ include_flags
         $ Cli.Flags.output
         $ Cli.Flags.optimize
         $ Cli.Flags.check_invariants
@@ -758,7 +775,7 @@ module Commands = struct
 
   let scalc
       options
-      link_modules
+      includes
       output
       optimize
       check_invariants
@@ -766,7 +783,7 @@ module Commands = struct
       closure_conversion
       ex_scope_opt =
     let prg, ctx, _ =
-      Passes.scalc options ~link_modules ~optimize ~check_invariants
+      Passes.scalc options ~includes ~optimize ~check_invariants
         ~avoid_exceptions ~closure_conversion
     in
     let _output_file, with_output = get_output_format options output in
@@ -795,7 +812,7 @@ module Commands = struct
       Term.(
         const scalc
         $ Cli.Flags.Global.options
-        $ Cli.Flags.link_modules
+        $ include_flags
         $ Cli.Flags.output
         $ Cli.Flags.optimize
         $ Cli.Flags.check_invariants
@@ -805,14 +822,14 @@ module Commands = struct
 
   let python
       options
-      link_modules
+      includes
       output
       optimize
       check_invariants
       avoid_exceptions
       closure_conversion =
     let prg, _, type_ordering =
-      Passes.scalc options ~link_modules ~optimize ~check_invariants
+      Passes.scalc options ~includes ~optimize ~check_invariants
         ~avoid_exceptions ~closure_conversion
     in
 
@@ -832,17 +849,17 @@ module Commands = struct
       Term.(
         const python
         $ Cli.Flags.Global.options
-        $ Cli.Flags.link_modules
+        $ include_flags
         $ Cli.Flags.output
         $ Cli.Flags.optimize
         $ Cli.Flags.check_invariants
         $ Cli.Flags.avoid_exceptions
         $ Cli.Flags.closure_conversion)
 
-  let r options link_modules output optimize check_invariants closure_conversion
+  let r options includes output optimize check_invariants closure_conversion
       =
     let prg, _, type_ordering =
-      Passes.scalc options ~link_modules ~optimize ~check_invariants
+      Passes.scalc options ~includes ~optimize ~check_invariants
         ~avoid_exceptions:false ~closure_conversion
     in
 
@@ -858,7 +875,7 @@ module Commands = struct
       Term.(
         const r
         $ Cli.Flags.Global.options
-        $ Cli.Flags.link_modules
+        $ include_flags
         $ Cli.Flags.output
         $ Cli.Flags.optimize
         $ Cli.Flags.check_invariants
diff --git a/compiler/driver.mli b/compiler/driver.mli
index a66134cf..af28226f 100644
--- a/compiler/driver.mli
+++ b/compiler/driver.mli
@@ -27,24 +27,24 @@ val main : unit -> unit
 module Passes : sig
   val surface :
     Cli.options ->
-    link_modules:string list ->
+    includes:File.Tree.t ->
     Surface.Ast.program * Cli.backend_lang
 
   val desugared :
     Cli.options ->
-    link_modules:string list ->
+    includes:File.Tree.t ->
     Desugared.Ast.program * Desugared.Name_resolution.context
 
   val scopelang :
     Cli.options ->
-    link_modules:string list ->
+    includes:File.Tree.t ->
     Shared_ast.untyped Scopelang.Ast.program
     * Desugared.Name_resolution.context
     * Desugared.Dependency.ExceptionsDependencies.t Desugared.Ast.ScopeDef.Map.t
 
   val dcalc :
     Cli.options ->
-    link_modules:string list ->
+    includes:File.Tree.t ->
     optimize:bool ->
     check_invariants:bool ->
     Shared_ast.typed Dcalc.Ast.program
@@ -53,7 +53,7 @@ module Passes : sig
 
   val lcalc :
     Cli.options ->
-    link_modules:string list ->
+    includes:File.Tree.t ->
     optimize:bool ->
     check_invariants:bool ->
     avoid_exceptions:bool ->
@@ -64,7 +64,7 @@ module Passes : sig
 
   val scalc :
     Cli.options ->
-    link_modules:string list ->
+    includes:File.Tree.t ->
     optimize:bool ->
     check_invariants:bool ->
     avoid_exceptions:bool ->
@@ -99,6 +99,8 @@ module Commands : sig
     string ->
     Desugared.Ast.ScopeDef.t
 
+  val include_flags : File.Tree.t Cmdliner.Term.t
+
   val commands : unit Cmdliner.Cmd.t list
   (** The list of built-in catala subcommands, as expected by
       [Cmdliner.Cmd.group] *)
diff --git a/compiler/plugins/api_web.ml b/compiler/plugins/api_web.ml
index 8c4261bf..abb13350 100644
--- a/compiler/plugins/api_web.ml
+++ b/compiler/plugins/api_web.ml
@@ -428,7 +428,7 @@ module To_jsoo = struct
 end
 
 let run
-    link_modules
+    includes
     output
     optimize
     check_invariants
@@ -438,7 +438,7 @@ let run
   if not options.Cli.trace then
     Message.raise_error "This plugin requires the --trace flag.";
   let prg, _, type_ordering =
-    Driver.Passes.lcalc options ~link_modules ~optimize ~check_invariants
+    Driver.Passes.lcalc options ~includes ~optimize ~check_invariants
       ~avoid_exceptions ~closure_conversion
   in
   let modname =
@@ -472,7 +472,7 @@ let run
 let term =
   let open Cmdliner.Term in
   const run
-  $ Cli.Flags.link_modules
+  $ Driver.Commands.include_flags
   $ Cli.Flags.output
   $ Cli.Flags.optimize
   $ Cli.Flags.check_invariants
diff --git a/compiler/plugins/dune b/compiler/plugins/dune
index 4f84c8e6..faeb5e19 100644
--- a/compiler/plugins/dune
+++ b/compiler/plugins/dune
@@ -38,13 +38,6 @@
  (flags (-linkall))
  (libraries shared_ast catala.driver ocamlgraph))
 
-(library
- (name modules)
- (public_name catala.plugins.modules)
- (synopsis "Catala plugin for experimental module handling tooling")
- (modules modules)
- (libraries shared_ast catala.driver))
-
 (documentation
  (package catala)
  (mld_files plugins))
diff --git a/compiler/plugins/explain.ml b/compiler/plugins/explain.ml
index dd3df927..ae5eba38 100644
--- a/compiler/plugins/explain.ml
+++ b/compiler/plugins/explain.ml
@@ -1385,12 +1385,12 @@ let options =
     $ Cli.Flags.output
     $ base_src_url)
 
-let run link_modules optimize ex_scope explain_options global_options =
+let run includes optimize ex_scope explain_options global_options =
   let prg, ctx, _ =
-    Driver.Passes.dcalc global_options ~link_modules ~optimize
+    Driver.Passes.dcalc global_options ~includes ~optimize
       ~check_invariants:false
   in
-  Interpreter.load_runtime_modules prg;
+  Interpreter.load_runtime_modules ~includes prg;
   let scope = Driver.Commands.get_scope_uid ctx ex_scope in
   (* let result_expr, env = interpret_program prg scope in *)
   let g, base_vars, env = program_to_graph explain_options prg scope in
@@ -1436,7 +1436,7 @@ let run link_modules optimize ex_scope explain_options global_options =
 let term =
   let open Cmdliner.Term in
   const run
-  $ Cli.Flags.link_modules
+  $ Driver.Commands.include_flags
   $ Cli.Flags.optimize
   $ Cli.Flags.ex_scope
   $ options
diff --git a/compiler/plugins/json_schema.ml b/compiler/plugins/json_schema.ml
index aae3d97e..2959350a 100644
--- a/compiler/plugins/json_schema.ml
+++ b/compiler/plugins/json_schema.ml
@@ -206,7 +206,7 @@ module To_json = struct
 end
 
 let run
-    link_modules
+    includes
     output
     optimize
     check_invariants
@@ -215,7 +215,7 @@ let run
     ex_scope
     options =
   let prg, ctx, _ =
-    Driver.Passes.lcalc options ~link_modules ~optimize ~check_invariants
+    Driver.Passes.lcalc options ~includes ~optimize ~check_invariants
       ~avoid_exceptions ~closure_conversion
   in
   let output_file, with_output =
@@ -233,7 +233,7 @@ let run
 let term =
   let open Cmdliner.Term in
   const run
-  $ Cli.Flags.link_modules
+  $ Driver.Commands.include_flags
   $ Cli.Flags.output
   $ Cli.Flags.optimize
   $ Cli.Flags.check_invariants
diff --git a/compiler/plugins/lazy_interp.ml b/compiler/plugins/lazy_interp.ml
index da114e55..368d7a81 100644
--- a/compiler/plugins/lazy_interp.ml
+++ b/compiler/plugins/lazy_interp.ml
@@ -257,11 +257,11 @@ let interpret_program (prg : ('dcalc, 'm) gexpr program) (scope : ScopeName.t) :
 
 (* -- Plugin registration -- *)
 
-let run link_modules optimize check_invariants ex_scope options =
+let run includes optimize check_invariants ex_scope options =
   let prg, ctx, _ =
-    Driver.Passes.dcalc options ~link_modules ~optimize ~check_invariants
+    Driver.Passes.dcalc options ~includes ~optimize ~check_invariants
   in
-  Interpreter.load_runtime_modules prg;
+  Interpreter.load_runtime_modules ~includes prg;
   let scope = Driver.Commands.get_scope_uid ctx ex_scope in
   let result_expr, _env = interpret_program prg scope in
   let fmt = Format.std_formatter in
@@ -270,7 +270,7 @@ let run link_modules optimize check_invariants ex_scope options =
 let term =
   let open Cmdliner.Term in
   const run
-  $ Cli.Flags.link_modules
+  $ Driver.Commands.include_flags
   $ Cli.Flags.optimize
   $ Cli.Flags.check_invariants
   $ Cli.Flags.ex_scope
diff --git a/compiler/plugins/modules.ml b/compiler/plugins/modules.ml
deleted file mode 100644
index ab2a711f..00000000
--- a/compiler/plugins/modules.ml
+++ /dev/null
@@ -1,233 +0,0 @@
-(* This file is part of the Catala compiler, a specification language for tax
-   and social benefits computation rules. Copyright (C) 2020 Inria, contributor:
-   Louis Gesbert <louis.gesbert@inria.fr>.
-
-   Licensed under the Apache License, Version 2.0 (the "License"); you may not
-   use this file except in compliance with the License. You may obtain a copy of
-   the License at
-
-   http://www.apache.org/licenses/LICENSE-2.0
-
-   Unless required by applicable law or agreed to in writing, software
-   distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
-   WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
-   License for the specific language governing permissions and limitations under
-   the License. *)
-
-open Catala_utils
-
-let action_flag =
-  let docs = "ACTIONS" in
-  let open Cmdliner.Arg in
-  required
-  & vflag None
-      [
-        ( Some `Compile,
-          info ["compile"] ~docs
-            ~doc:
-              "Compiles a Catala file into a module: a $(b,.cmxs) file that \
-               can be used by the Catala interpreter."
-          (* "and $(b,cmo) and $(b,cmx) files that can be linked into an OCaml
-             program" *) );
-        ( Some `Link,
-          info ["link"] ~docs
-            ~doc:
-              "Compiles and links a catala program into a binary (using the \
-               ocaml backend). Specify a main scope using the $(b,--scope) \
-               flag to be run upon execution. This is still pretty useless at \
-               the moment besides for testing purposes, as there is no way to \
-               feed input to the generated program, and the output will be \
-               silent. Assertions will be checked, though." );
-      ]
-
-let gen_ocaml options link_modules optimize check_invariants main =
-  let prg, ctx, type_ordering =
-    Driver.Passes.lcalc options ~link_modules ~optimize ~check_invariants
-      ~avoid_exceptions:false ~closure_conversion:false
-  in
-  let exec_scope = Option.map (Driver.Commands.get_scope_uid ctx) main in
-  let filename, with_output =
-    Driver.Commands.get_output_format options ~ext:".ml" None
-  in
-  with_output
-  @@ fun ppf ->
-  Lcalc.To_ocaml.format_program ppf ?exec_scope prg type_ordering;
-  Option.get filename
-
-let run_process cmd args =
-  Message.emit_debug "Running @[<hov 4>@{<yellow>@{<bold>%s@} %a@}@}@]" cmd
-    (Format.pp_print_list ~pp_sep:Format.pp_print_space Format.pp_print_string)
-    args;
-  match
-    Unix.waitpid []
-      (Unix.create_process cmd
-         (Array.of_list (cmd :: args))
-         Unix.stdin Unix.stdout Unix.stderr)
-  with
-  | _, Unix.WEXITED 0 -> ()
-  | _, _ -> Message.raise_error "Child process @{<bold>%s@} failed" cmd
-
-let with_flag flag args =
-  List.fold_right (fun p acc -> flag :: p :: acc) args []
-
-let ocaml_libdir =
-  lazy
-    (try String.trim (File.process_out "opam" ["var"; "lib"])
-     with Failure _ -> (
-       try String.trim (File.process_out "ocamlc" ["-where"])
-       with Failure _ -> (
-         match File.(check_directory (dirname Sys.argv.(0) /../ "lib")) with
-         | Some d -> d
-         | None ->
-           Message.raise_error
-             "Could not locate the OCaml library directory, make sure OCaml or \
-              opam is installed")))
-
-let rec find_catala_project_root dir =
-  if Sys.file_exists File.(dir / "catala.opam") then Some dir
-  else
-    let dir' = File.dirname dir in
-    if dir' = dir then None else find_catala_project_root dir'
-
-let runtime_dir =
-  lazy
-    (let d =
-       match find_catala_project_root (Sys.getcwd ()) with
-       | Some root ->
-         (* Relative dir when running from catala source *)
-         File.(
-           root
-           / "_build"
-           / "install"
-           / "default"
-           / "lib"
-           / "catala"
-           / "runtime_ocaml")
-       | None -> (
-         match
-           File.check_directory
-             File.(dirname Sys.argv.(0) /../ "lib" / "catala" / "runtime_ocaml")
-         with
-         | Some d -> d
-         | None -> File.(Lazy.force ocaml_libdir / "catala" / "runtime"))
-     in
-     match File.check_directory d with
-     | Some dir ->
-       Message.emit_debug "Catala runtime libraries found at @{<bold>%s@}." dir;
-       dir
-     | None ->
-       Message.raise_error
-         "@[<hov>Could not locate the Catala runtime library.@ Make sure that \
-          either catala is correctly installed,@ or you are running from the \
-          root of a compiled source tree.@]")
-
-let compile options link_modules optimize check_invariants =
-  let modname =
-    match options.Cli.input_file with
-    (* TODO: extract module name from directives *)
-    | FileName n -> Driver.modname_of_file n
-    | _ -> Message.raise_error "Input must be a file name for this command"
-  in
-  let basename = String.uncapitalize_ascii modname in
-  let ml_file = gen_ocaml options link_modules optimize check_invariants None in
-  let flags = ["-I"; Lazy.force runtime_dir] in
-  let shared_out = File.((ml_file /../ basename) ^ ".cmxs") in
-  Message.emit_debug "Compiling OCaml shared object file @{<bold>%s@}..."
-    shared_out;
-  run_process "ocamlopt" ("-shared" :: ml_file :: "-o" :: shared_out :: flags);
-  (* let byte_out = basename ^ ".cmo" in
-   * Message.emit_debug "Compiling OCaml byte-code object file @{<bold>%s@}..." byte_out;
-   * run_process "ocamlc" ("-c" :: ml_file :: "-o" :: byte_out :: flags);
-   * let native_out = basename ^ ".cmx" in
-   * Message.emit_debug "Compiling OCaml native object file @{<bold>%s@}..." native_out;
-   * run_process "ocamlopt" ("-c" :: ml_file :: "-o" :: native_out ::flags); *)
-  Message.emit_debug "Done."
-
-let link options link_modules optimize check_invariants output ex_scope_opt =
-  let ml_file =
-    gen_ocaml options link_modules optimize check_invariants ex_scope_opt
-  in
-  (* NOTE: assuming native target at the moment *)
-  let cmd = "ocamlopt" in
-  let ocaml_libdir = Lazy.force ocaml_libdir in
-  let runtime_dir = Lazy.force runtime_dir in
-  (* Recursive dependencies are expanded manually here. A shorter version would
-     use [ocamlfind ocalmopt -linkpkg -package] with just ppx_yojson_conv_lib,
-     zarith and dates_calc *)
-  let link_libs =
-    [
-      "biniou";
-      "easy-format";
-      "yojson";
-      "ppx_yojson_conv_lib";
-      "zarith";
-      "dates_calc";
-    ]
-  in
-  let link_libdirs =
-    List.map
-      (fun lib ->
-        match File.(check_directory (ocaml_libdir / lib)) with
-        | None ->
-          Message.raise_error
-            "Required OCaml library not found at @{<bold>%s@}.@ Try `opam \
-             install %s'"
-            File.(ocaml_libdir / lib)
-            lib
-        | Some l -> l)
-      link_libs
-  in
-  let runtime_lib = File.(runtime_dir / "runtime_ocaml.cmxa") in
-  let modules =
-    List.map (fun m -> Filename.remove_extension m ^ ".cmx") link_modules
-  in
-  let output =
-    match output with
-    | Some o -> o
-    | None -> Filename.remove_extension ml_file ^ ".exe"
-  in
-  let args =
-    with_flag "-I" link_libdirs
-    @ with_flag "-I"
-        (List.sort_uniq compare (List.map Filename.dirname modules))
-    @ List.map
-        (fun lib -> String.map (function '-' -> '_' | c -> c) lib ^ ".cmxa")
-        link_libs
-    @ ("-I" :: runtime_dir :: runtime_lib :: modules)
-    @ [ml_file; "-o"; output]
-  in
-  run_process cmd args;
-  Message.emit_result "Successfully generated @{<bold>%s@}" output
-(* Compile from ml and link the modules cmx. => ocamlfind ocamlopt -linkpkg
-   -package ppx_yojson_conv_lib -package zarith -package dates_calc -I
-   _build/default/runtimes/ocaml/.runtime_ocaml.objs/byte
-   _build/default/runtimes/ocaml/runtime_ocaml.cmxa ext.cmx extuse.ml *)
-
-let run
-    action
-    link_modules
-    optimize
-    check_invariants
-    output
-    ex_scope_opt
-    options =
-  match action with
-  | `Compile -> compile options link_modules optimize check_invariants
-  | `Link ->
-    link options link_modules optimize check_invariants ex_scope_opt output
-
-let term =
-  let open Cmdliner.Term in
-  const run
-  $ action_flag
-  $ Cli.Flags.link_modules
-  $ Cli.Flags.optimize
-  $ Cli.Flags.check_invariants
-  $ Cli.Flags.ex_scope_opt
-  $ Cli.Flags.output
-
-let () =
-  Driver.Plugin.register "module" term
-    ~doc:
-      "This plugin provides a few experimental tools related to module \
-       generation and compilation"
diff --git a/compiler/plugins/python.ml b/compiler/plugins/python.ml
index 4c15aacb..85ad1f97 100644
--- a/compiler/plugins/python.ml
+++ b/compiler/plugins/python.ml
@@ -23,7 +23,7 @@
 open Catala_utils
 
 let run
-    link_modules
+    includes
     output
     optimize
     check_invariants
@@ -32,7 +32,7 @@ let run
     options =
   let open Driver.Commands in
   let prg, _, type_ordering =
-    Driver.Passes.scalc options ~link_modules ~optimize ~check_invariants
+    Driver.Passes.scalc options ~includes ~optimize ~check_invariants
       ~avoid_exceptions ~closure_conversion
   in
 
@@ -45,7 +45,7 @@ let run
 let term =
   let open Cmdliner.Term in
   const run
-  $ Cli.Flags.link_modules
+  $ Driver.Commands.include_flags
   $ Cli.Flags.output
   $ Cli.Flags.optimize
   $ Cli.Flags.check_invariants
diff --git a/compiler/shared_ast/interpreter.ml b/compiler/shared_ast/interpreter.ml
index a07f2d11..4d8867b2 100644
--- a/compiler/shared_ast/interpreter.ml
+++ b/compiler/shared_ast/interpreter.ml
@@ -940,29 +940,47 @@ let interpret_program_dcalc p s : (Uid.MarkedString.info * ('a, 'm) gexpr) list
    reflect that. *)
 let evaluate_expr ctx lang e = delcustom (evaluate_expr ctx lang (addcustom e))
 
-let load_runtime_modules prg =
-  match ModuleName.Map.keys prg.decl_ctx.ctx_modules with
-  | [] -> ()
-  | modules ->
-    Message.emit_debug "Loading shared modules... %a"
-      (fun ppf -> ModuleName.Map.format_keys ppf)
-      prg.decl_ctx.ctx_modules;
-    List.iter
-      (fun m ->
-        let srcfile = Pos.get_file (ModuleName.pos m) in
-        let obj_file =
-          File.((srcfile /../ ModuleName.to_string m) ^ ".cmo")
-          |> Dynlink.adapt_filename
-        in
-        let obj_file =
-          match Cli.globals.build_dir with
-          | None -> obj_file
-          | Some d -> File.(d / obj_file)
-        in
-        try Dynlink.loadfile obj_file
-        with Dynlink.Error dl_err ->
-          Message.raise_error
-            "Could not load module %a, has it been suitably compiled?@;\
-             <1 2>@[<hov>%a@]" ModuleName.format m Format.pp_print_text
-            (Dynlink.error_message dl_err))
-      modules
+let load_runtime_modules ~build_dirs prg =
+  let load m =
+    let obj_base =
+      Dynlink.adapt_filename File.(Pos.get_file (ModuleName.pos m) /../ ModuleName.to_string m ^ ".cmo")
+    in
+    let possible_files = List.map File.(fun d -> d / obj_base) build_dirs in
+    match List.filter Sys.file_exists possible_files with
+    | [] ->
+      Message.raise_spanned_error
+        ~span_msg:(fun ppf -> Format.pp_print_string ppf "Module defined here")
+        (ModuleName.pos m)
+        "Compiled OCaml object %a not found. Make sure it has been suitably compiled, and use @{<blue>-I DIR@} if necessary." File.format obj_base
+    | [f] ->
+      (try Dynlink.loadfile f
+       with Dynlink.Error dl_err ->
+         Message.raise_error
+           "Error loading compiled module from %a:@;\
+            <1 2>@[<hov>%a@]" File.format f
+           Format.pp_print_text
+           (Dynlink.error_message dl_err))
+    | fs ->
+      Message.raise_spanned_error
+        ~span_msg:(fun ppf -> Format.pp_print_string ppf "Module defined here")
+        (ModuleName.pos m)
+        "@[<v>Multiple compiled OCaml objects for %a found:@,- %a@]"
+        ModuleName.format m
+        (Format.pp_print_list ~pp_sep:(fun ppf () -> Format.fprintf ppf "@,- ")
+           File.format)
+        fs
+  in
+  let rec aux loaded decl_ctx =
+    ModuleName.Map.fold (fun mname sub_decl_ctx loaded ->
+        if ModuleName.Set.mem mname loaded then loaded else
+          let loaded = ModuleName.Set.add mname loaded in
+          let loaded = aux loaded sub_decl_ctx in
+          load mname;
+          loaded)
+      decl_ctx.ctx_modules loaded
+  in
+  Message.emit_debug "Loading shared modules... %a"
+    (fun ppf -> ModuleName.Map.format_keys ppf)
+    prg.decl_ctx.ctx_modules;
+  let (_loaded: ModuleName.Set.t) = aux ModuleName.Set.empty prg.decl_ctx in
+  ()
diff --git a/compiler/shared_ast/interpreter.mli b/compiler/shared_ast/interpreter.mli
index d95cc387..2f2fcecc 100644
--- a/compiler/shared_ast/interpreter.mli
+++ b/compiler/shared_ast/interpreter.mli
@@ -72,8 +72,8 @@ val interpret_program_lcalc :
     providing for each argument a thunked empty default. Returns a list of all
     the computed values for the scope variables of the executed scope. *)
 
-val load_runtime_modules : _ program -> unit
+val load_runtime_modules : build_dirs:File.t list -> _ program -> unit
 (** Dynlink the runtime modules required by the given program, in order to make
-    them callable by the interpreter. If Cli.globals.build_dir is specified, the
-    runtime module names (as obtained by looking up the positions in the
-    program's module bindings) are assumed to be relative and looked up there. *)
+    them callable by the interpreter.
+
+    The specified build dirs are used as prefixes to the catala files defining the modules: with {[["."; "_build"]]}, this means that the compiled artifact of [foo/bar.catala_en] will be searched in [foo/bar.cmxs] and [_build/foo/bar.cmxs] *)
diff --git a/compiler/surface/parser_driver.ml b/compiler/surface/parser_driver.ml
index d8b0c1a2..23dad967 100644
--- a/compiler/surface/parser_driver.ml
+++ b/compiler/surface/parser_driver.ml
@@ -273,7 +273,10 @@ and expand_includes
         match command with
         | Ast.ModuleDef id -> (
           match acc.Ast.program_module_name with
-          | None -> { acc with Ast.program_module_name = Some id }
+          | None ->
+            { acc with Ast.program_module_name = Some id;
+                       Ast.program_items = command :: acc.Ast.program_items;
+            }
           | Some id2 ->
             Message.raise_multispanned_error
               [None, Mark.get id; None, Mark.get id2]