diff --git a/infer/src/backend/CommandLineOption.ml b/infer/src/backend/CommandLineOption.ml
index f01402181..03d31a647 100644
--- a/infer/src/backend/CommandLineOption.ml
+++ b/infer/src/backend/CommandLineOption.ml
@@ -12,6 +12,7 @@
 open! Utils
 
 module F = Format
+module YBU = Yojson.Basic.Util
 
 
 (* Each command line option may appear in the --help list of any executable, these tags are used to
@@ -28,7 +29,11 @@ let current_exe =
   | _ -> T
 
 
-type desc = { long: string; short: string; meta: string; doc: string; spec: Arg.spec }
+type desc = {
+  long: string; short: string; meta: string; doc: string; spec: Arg.spec;
+  (** how to go from an option in the json config file to a list of command-line options *)
+  decode_json: Yojson.Basic.json -> string list ;
+}
 
 let dashdash long =
   match long with
@@ -125,7 +130,7 @@ let add exes desc =
     ) exe_desc_lists
 
 let mk ?(deprecated=[]) ?(exes=[])
-    ~long ?(short="") ~default ~meta doc ~default_to_string ~mk_setter ~mk_spec =
+    ~long ?(short="") ~default ~meta doc ~default_to_string ~decode_json ~mk_setter ~mk_spec =
   let variable = ref default in
   let closure = mk_setter variable in
   let setter str =
@@ -136,7 +141,7 @@ let mk ?(deprecated=[]) ?(exes=[])
     let default_string = default_to_string default in
     if default_string = "" then doc
     else doc ^ " (default: " ^ default_string ^ ")" in
-  let desc = {long; short; meta; doc; spec} in
+  let desc = {long; short; meta; doc; spec; decode_json} in
   (* add desc for long option, with documentation (which includes any short option) for exes *)
   add exes desc ;
   (* add desc for short option only for parsing, without documentation *)
@@ -153,11 +158,16 @@ type 'a t =
   ?exes:exe list -> ?meta:string -> Arg.doc ->
   'a
 
+let string_json_decoder ~long json = [dashdash long; YBU.to_string json]
+
+let list_json_decoder json_decoder json = IList.flatten (YBU.convert_each json_decoder json)
+
 let mk_set var value ?(deprecated=[]) ~long ?short ?exes ?(meta="") doc =
   let setter () = var := value in
   ignore(
     mk ~deprecated ~long ?short ~default:() ?exes ~meta doc
       ~default_to_string:(fun () -> "")
+      ~decode_json:(string_json_decoder ~long)
       ~mk_setter:(fun _ _ -> setter ())
       ~mk_spec:(fun _ -> Arg.Unit setter) )
 
@@ -165,6 +175,7 @@ let mk_option ?(default=None) ?(default_to_string=fun _ -> "") ~f
     ?(deprecated=[]) ~long ?short ?exes ?(meta="") doc =
   mk ~deprecated ~long ?short ~default ?exes ~meta doc
     ~default_to_string
+    ~decode_json:(string_json_decoder ~long)
     ~mk_setter:(fun var str -> var := f str)
     ~mk_spec:(fun set -> Arg.String set)
 
@@ -199,10 +210,16 @@ let mk_bool ?(deprecated_no=[]) ?(default=false) ?(f=fun b -> b)
   let mk_spec set = Arg.Unit (fun () -> set "") in
   let var =
     mk ~long ?short ~deprecated ~default ?exes
-      ~meta doc ~default_to_string ~mk_setter:(fun var _ -> var := f true) ~mk_spec in
+      ~meta doc ~default_to_string ~mk_setter:(fun var _ -> var := f true)
+      ~decode_json:(fun json ->
+          [dashdash (if YBU.to_bool json then long else nolong)])
+      ~mk_spec in
   ignore(
     mk ~long:nolong ?short:noshort ~deprecated:deprecated_no ~default:(not default) ?exes
-      ~meta nodoc ~default_to_string ~mk_setter:(fun _ _ -> var := f false) ~mk_spec );
+      ~meta nodoc ~default_to_string ~mk_setter:(fun _ _ -> var := f false)
+      ~decode_json:(fun json ->
+          [dashdash (if YBU.to_bool json then nolong else long)])
+      ~mk_spec );
   var
 
 let mk_bool_group ?(deprecated_no=[]) ?(default=false)
@@ -217,18 +234,21 @@ let mk_int ~default ?(deprecated=[]) ~long ?short ?exes ?(meta="") doc =
   mk ~deprecated ~long ?short ~default ?exes ~meta doc
     ~default_to_string:string_of_int
     ~mk_setter:(fun var str -> var := (int_of_string str))
+    ~decode_json:(string_json_decoder ~long)
     ~mk_spec:(fun set -> Arg.String set)
 
 let mk_float ~default ?(deprecated=[]) ~long ?short ?exes ?(meta="") doc =
   mk ~deprecated ~long ?short ~default ?exes ~meta doc
     ~default_to_string:string_of_float
     ~mk_setter:(fun var str -> var := (float_of_string str))
+    ~decode_json:(string_json_decoder ~long)
     ~mk_spec:(fun set -> Arg.String set)
 
 let mk_string ~default ?(f=fun s -> s) ?(deprecated=[]) ~long ?short ?exes ?(meta="") doc =
   mk ~deprecated ~long ?short ~default ?exes ~meta doc
     ~default_to_string:(fun s -> s)
     ~mk_setter:(fun var str -> var := f str)
+    ~decode_json:(string_json_decoder ~long)
     ~mk_spec:(fun set -> Arg.String set)
 
 let mk_string_opt ?default ?(f=fun s -> s) ?(deprecated=[]) ~long ?short ?exes ?(meta="") doc =
@@ -241,6 +261,7 @@ let mk_string_list ?(default=[]) ?(f=fun s -> s)
   mk ~deprecated ~long ?short ~default ?exes ~meta doc
     ~default_to_string:(String.concat ", ")
     ~mk_setter:(fun var str -> var := (f str) :: !var)
+    ~decode_json:(list_json_decoder (string_json_decoder ~long))
     ~mk_spec:(fun set -> Arg.String set)
 
 let mk_symbol ~default ~symbols ?(deprecated=[]) ~long ?short ?exes ?(meta="") doc =
@@ -251,6 +272,7 @@ let mk_symbol ~default ~symbols ?(deprecated=[]) ~long ?short ?exes ?(meta="") d
   mk ~deprecated ~long ?short ~default ?exes ~meta doc
     ~default_to_string:(fun s -> to_string s)
     ~mk_setter:(fun var str -> var := of_string str)
+    ~decode_json:(string_json_decoder ~long)
     ~mk_spec:(fun set -> Arg.Symbol (strings, set))
 
 let mk_symbol_opt ~symbols ?(deprecated=[]) ~long ?short ?exes ?(meta="") doc =
@@ -259,6 +281,7 @@ let mk_symbol_opt ~symbols ?(deprecated=[]) ~long ?short ?exes ?(meta="") doc =
   mk ~deprecated ~long ?short ~default:None ?exes ~meta doc
     ~default_to_string:(fun _ -> "")
     ~mk_setter:(fun var str -> var := Some (of_string str))
+    ~decode_json:(string_json_decoder ~long)
     ~mk_spec:(fun set -> Arg.Symbol (strings, set))
 
 let mk_symbol_seq ?(default=[]) ~symbols ?(deprecated=[]) ~long ?short ?exes ?(meta="") doc =
@@ -269,6 +292,9 @@ let mk_symbol_seq ?(default=[]) ~symbols ?(deprecated=[]) ~long ?short ?exes ?(m
     ~default_to_string:(fun syms -> String.concat " " (IList.map to_string syms))
     ~mk_setter:(fun var str_seq ->
         var := IList.map of_string (Str.split (Str.regexp_string ",") str_seq))
+    ~decode_json:(fun json ->
+        [dashdash long;
+         String.concat "," (YBU.convert_each YBU.to_string json)])
     ~mk_spec:(fun set -> Arg.String set)
 
 let anon_fun = ref (fun arg -> raise (Arg.Bad ("unexpected anonymous argument: " ^ arg)))
@@ -279,6 +305,38 @@ let mk_anon () =
   anon
 
 
+(* begin temporarily export inferconfig_json while .inferconfig-specific options still exist *)
+let inferconfig_json = ref (`Assoc [])
+(* end temporarily export inferconfig_json *)
+
+let decode_inferconfig_to_argv path =
+  let json = match read_optional_json_file path with
+    | Ok json ->
+        (* begin temporarily export inferconfig_json while
+           .inferconfig-specific options still exist *)
+        inferconfig_json := json ;
+        (* end temporarily export inferconfig_json *)
+        json
+    | Error msg ->
+        F.eprintf "WARNING: Could not read or parse Infer config in %s:@\n%s@." path msg ;
+        `Assoc [] in
+  let desc_list = !(IList.assoc ( = ) current_exe exe_desc_lists) in
+  let json_config = YBU.to_assoc json in
+  let one_config_item result (key, json_val) =
+    try
+      let {decode_json} = IList.find (fun {long} -> string_equal key long) desc_list in
+      decode_json json_val @ result
+    with
+    | Not_found ->
+        (* TODO: have all json options be regular options as well. When this is done, we can show a
+           warning if a json key is not a valid option. *)
+        result
+    | YBU.Type_error (msg, json) ->
+        F.eprintf "WARNING: while reading config file %s:@\nIll-formed value %s for option %s: %s@."
+          path (Yojson.Basic.to_string json) key msg ;
+        result in
+  IList.fold_left one_config_item [] json_config
+
 
 (** [sep_char] is used to separate elements of argv when encoded into environment variables *)
 let sep_char = '^'
@@ -308,7 +366,7 @@ let prefix_before_rest args =
   prefix_before_rest_ [] args
 
 
-let parse ?(incomplete=false) env_var exe_usage =
+let parse ?(incomplete=false) ?config_file env_var exe_usage =
   let curr_speclist = ref []
   and full_speclist = ref []
   in
@@ -322,12 +380,15 @@ let parse ?(incomplete=false) env_var exe_usage =
     exit status
   in
   let help_desc_list =
-    [ { long = "help"; short = ""; meta = ""; spec = Arg.Unit (fun () -> curr_usage 0);
+    [ { long = "help"; short = ""; meta = ""; decode_json = (fun _ -> []);
+        spec = Arg.Unit (fun () -> curr_usage 0);
         doc = "Display this list of options" }
-    ; { long = "help-full"; short = ""; meta = ""; spec = Arg.Unit (fun () -> full_usage 0);
+    ; { long = "help-full"; short = ""; meta = ""; decode_json = (fun _ -> []);
+        spec = Arg.Unit (fun () -> full_usage 0);
         doc = "Display the full list of options, including internal and experimental options" }
     ] in
-  let section heading speclist =
+  let normalize speclist =
+    let speclist = help_desc_list @ speclist in
     let norm k =
       let len = String.length k in
       if len > 3 && String.sub k 0 3 = "no-" then String.sub k 3 (len - 3) else k in
@@ -338,27 +399,20 @@ let parse ?(incomplete=false) env_var exe_usage =
       | _, "--" -> -1
       | _ -> String.compare (norm x) (norm y) in
     let sort speclist = IList.sort compare_specs speclist in
-    let add_heading speclist =
-      match heading with
-      | Some heading ->
-          let doc = "\n  " ^ heading ^ "\n" in
-          { doc; long = ""; short = ""; meta = ""; spec = Arg.Unit (fun () -> ()) } :: speclist
-      | None ->
-          speclist in
     let suppress_help speclist =
       ("-help", Arg.Unit (fun () -> raise (Arg.Bad "unknown option '-help'")), "") :: speclist in
-    suppress_help (align ~limit:32 (add_heading (sort speclist)))
+    suppress_help (align ~limit:32 (sort speclist))
   in
   let curr_desc_list = IList.assoc ( = ) current_exe exe_desc_lists
   in
   (* curr_speclist includes args for current exe with docs, and all other args without docs, so
      that all args can be parsed, but --help and parse failures only show external args for
      current exe *)
-  curr_speclist := (section None (help_desc_list @ !curr_desc_list))
+  curr_speclist := normalize !curr_desc_list
   ;
   assert( check_no_duplicates !curr_speclist )
   ;
-  full_speclist := (section None (help_desc_list @ !full_desc_list))
+  full_speclist := normalize !full_desc_list
   ;
   let env_args = decode_env_to_argv (try Unix.getenv env_var with Not_found -> "") in
   (* begin transitional support for INFERCLANG_ARGS *)
@@ -368,10 +422,16 @@ let parse ?(incomplete=false) env_var exe_usage =
   let env_args = c_args @ env_args in
   (* end transitional support for INFERCLANG_ARGS *)
   let exe_name, env_cl_args = prepend_to_argv env_args in
+  let all_args = match config_file with
+    | None -> env_cl_args
+    | Some path ->
+        let json_args = decode_inferconfig_to_argv path in
+        (* read .inferconfig first, as both env vars and command-line options overwrite it *)
+        json_args @ env_cl_args in
   let current = ref 0 in
   let rec parse_loop () =
     try
-      Arg.parse_argv_dynamic ~current (Array.of_list (exe_name :: env_cl_args))
+      Arg.parse_argv_dynamic ~current (Array.of_list (exe_name :: all_args))
         curr_speclist !anon_fun usage_msg
     with
     | Arg.Bad _ when incomplete -> parse_loop ()
@@ -380,5 +440,5 @@ let parse ?(incomplete=false) env_var exe_usage =
   in
   parse_loop () ;
   if not incomplete then
-    Unix.putenv env_var (encode_argv_to_env (prefix_before_rest env_cl_args)) ;
+    Unix.putenv env_var (encode_argv_to_env (prefix_before_rest all_args)) ;
   curr_usage
diff --git a/infer/src/backend/CommandLineOption.mli b/infer/src/backend/CommandLineOption.mli
index 7ec992200..574816cf0 100644
--- a/infer/src/backend/CommandLineOption.mli
+++ b/infer/src/backend/CommandLineOption.mli
@@ -11,6 +11,10 @@
 
 open! Utils
 
+(* begin temporarily export inferconfig_json while .inferconfig-specific options still exist *)
+val inferconfig_json : Yojson.Basic.json ref
+(* end temporarily export inferconfig_json *)
+
 type exe = A | C | J | L | P | T
 
 val current_exe : exe
@@ -89,8 +93,11 @@ val mk_anon :
 
 (** [parse env_var exe_usage] parses command line arguments as specified by preceding calls to the
     [mk_*] functions, and returns a function that prints the usage message and help text then exits.
-    The decoded value of environment variable [env_var] is prepended to [Sys.argv] before parsing.
-    Therefore arguments passed on the command line supercede those specified in the environment
-    variable.  WARNING: If an argument appears both in the environment variable and on the command
-    line, it will be interpreted twice. *)
-val parse : ?incomplete:bool -> string -> (exe -> Arg.usage_msg) -> (int -> 'a)
+    The decoded values of the inferconfig file [config_file], if provided, and of the environment
+    variable [env_var] are prepended to [Sys.argv] before parsing.  Therefore arguments passed on
+    the command line supersede those specified in the environment variable, which themselves
+    supersede those passed via the config file.  WARNING: An argument will be interpreted as many
+    times as it appears in all of the config file, the environment variable, and the command
+    line. *)
+val parse : ?incomplete:bool -> ?config_file:string ->
+  string -> (exe -> Arg.usage_msg) -> (int -> 'a)
diff --git a/infer/src/backend/config.ml b/infer/src/backend/config.ml
index 18db9fc66..0e0093d10 100644
--- a/infer/src/backend/config.ml
+++ b/infer/src/backend/config.ml
@@ -952,7 +952,7 @@ let post_parsing_initialization () =
 
 
 let parse_args_and_return_usage_exit =
-  let usage_exit = CLOpt.parse "INFER_ARGS" exe_usage in
+  let usage_exit = CLOpt.parse ~config_file:inferconfig_path "INFER_ARGS" exe_usage in
   if !debug || (!developer_mode && not (CLOpt.current_exe = CLOpt.P)) then
     prerr_endline
       ((Filename.basename Sys.executable_name) ^ " got args "
@@ -1055,22 +1055,15 @@ and write_html = !write_html
 and xml_specs = !xml_specs
 and zip_libraries = !zip_libraries
 
-let inferconfig_json =
-  lazy (
-    match read_optional_json_file inferconfig_path with
-    | Ok json -> json
-    | Error msg ->
-        F.fprintf F.err_formatter "Could not read or parse Infer config in %s:@\n%s@."
-          inferconfig_path msg;
-        exit 1)
+let inferconfig_json = lazy !CLOpt.inferconfig_json
 
 and suppress_warnings_json = lazy (
   let error msg =
-    F.fprintf F.err_formatter "There was an issue reading the option %s.@\n"
+    F.eprintf "There was an issue reading the option %s.@\n"
       suppress_warnings_annotations_long ;
-    F.fprintf F.err_formatter "If you did not call %s directly, this is likely a bug in Infer.@\n"
+    F.eprintf "If you did not call %s directly, this is likely a bug in Infer.@\n"
       (Filename.basename Sys.executable_name) ;
-    F.fprintf F.err_formatter "%s@." msg ;
+    F.eprintf "%s@." msg ;
     exit 1 in
   match !suppress_warnings_out with
   | Some path -> (
diff --git a/infer/src/backend/inferprint.ml b/infer/src/backend/inferprint.ml
index b4d68309c..6599b88ca 100644
--- a/infer/src/backend/inferprint.ml
+++ b/infer/src/backend/inferprint.ml
@@ -823,7 +823,7 @@ module AnalysisResults = struct
     (* find spec files specified by command-line arguments *)
     IList.iter (fun arg ->
         if not (Filename.check_suffix arg Config.specs_files_suffix) && arg <> "."
-        then print_usage_exit "arguments must be .specs files"
+        then print_usage_exit ("file "^ arg ^ ": arguments must be .specs files")
       ) Config.anon_args ;
     (match Config.source_file_copy with
      | Some s -> source_file_copy := Some (DB.abs_source_file_from_path s)