nixpkgs/pkgs/development/tools/comby/comby.patch

diff --git a/comby-kernel.opam b/comby-kernel.opam
index 828c5a3..00f6c3d 100644
--- a/comby-kernel.opam
+++ b/comby-kernel.opam
@@ -20,7 +20,7 @@ build: [
 depends: [
   "dune" {>= "2.8.0"}
   "ocaml" {>= "4.08.1"}
-  "core_kernel"
+  "core_kernel" {>= "v0.15.0"}
   "mparser" {>= "1.3"}
   "mparser-pcre"
   "ppx_deriving"
diff --git a/comby-semantic.opam b/comby-semantic.opam
index cb9dcc7..443749f 100644
--- a/comby-semantic.opam
+++ b/comby-semantic.opam
@@ -20,7 +20,7 @@ build: [
 depends: [
   "dune" {>= "2.8.0"}
   "ocaml" {>= "4.08.1"}
-  "core_kernel"
+  "core_kernel" {>= "v0.15.0"}
   "ppx_deriving"
   "lwt"
   "cohttp"
diff --git a/comby.opam b/comby.opam
index 98bdc19..d45892c 100644
--- a/comby.opam
+++ b/comby.opam
@@ -31,7 +31,7 @@ depends: [
   "cohttp-lwt-unix"
   "comby-kernel" {= "1.7.0"}
   "comby-semantic" {= "1.7.0"}
-  "core"
+  "core" {>= "v0.15.0"}
   "hack_parallel" {arch != "arm32" & arch != "arm64"}
   "lwt"
   "lwt_react"
diff --git a/dune b/dune
index 53b1312..a71571a 100644
--- a/dune
+++ b/dune
@@ -1,6 +1,8 @@
 (env
  (dev
-  (flags (:standard -w A-3-4-32-34-37-39-40-41-42-44-45-48-49-50-57-60-66-67)))
+  (flags
+   (:standard -w A-3-4-32-34-37-39-40-41-42-44-45-48-49-50-57-60-66-67)))
  (release
-  (flags (:standard -w A-3-4-32-34-37-39-40-41-42-44-45-48-49-50-57-60-66-67))
- (ocamlopt_flags (-O3))))
+  (flags
+   (:standard -w A-3-4-32-34-37-39-40-41-42-44-45-48-49-50-57-60-66-67))
+  (ocamlopt_flags (-O3))))
diff --git a/lib/app/configuration/command_configuration.ml b/lib/app/configuration/command_configuration.ml
index eed8420..aea4dfa 100644
--- a/lib/app/configuration/command_configuration.ml
+++ b/lib/app/configuration/command_configuration.ml
@@ -16,21 +16,21 @@ type 'a next =
 
 let fold_directory ?(sorted=false) root ~init ~f =
   let rec aux acc absolute_path depth =
-    if Sys.is_file absolute_path = `Yes then
+    if Sys_unix.is_file absolute_path = `Yes then
       match f acc ~depth ~absolute_path ~is_file:true with
       | Continue acc
       | Skip acc -> acc
-    else if Sys.is_directory absolute_path = `Yes then
+    else if Sys_unix.is_directory absolute_path = `Yes then
       match f acc ~depth ~absolute_path ~is_file:false with
       | Skip acc -> acc
       | Continue acc ->
         let dir_contents =
           if Option.is_some (Sys.getenv "COMBY_TEST") || sorted then
-            Sys.ls_dir absolute_path
+            Sys_unix.ls_dir absolute_path
             |> List.sort ~compare:String.compare
             |> List.rev
           else
-            Sys.ls_dir absolute_path
+            Sys_unix.ls_dir absolute_path
         in
         List.fold dir_contents ~init:acc ~f:(fun acc subdir ->
             aux acc (Filename.concat absolute_path subdir) (depth + 1))
@@ -50,8 +50,8 @@ let parse_source_directories
   let exact_file_paths, file_patterns =
     List.partition_map file_filters ~f:(fun path ->
         let is_exact path =
-          (String.contains path '/' && Sys.is_file path = `Yes)
-          || (Sys.is_file ("." ^/ path) = `Yes) (* See if it matches something in the current directory *)
+          (String.contains path '/' && Sys_unix.is_file path = `Yes)
+          || (Sys_unix.is_file ("." ^/ path) = `Yes) (* See if it matches something in the current directory *)
         in
         if is_exact path then Either.First path else Either.Second path)
   in
@@ -167,8 +167,8 @@ let parse_templates ?metasyntax ?(warn_for_missing_file_in_dir = false) paths =
   let f acc ~depth:_ ~absolute_path ~is_file =
     let is_leaf_directory absolute_path =
       not is_file &&
-      Sys.ls_dir absolute_path
-      |> List.for_all ~f:(fun path -> Sys.is_directory (absolute_path ^/ path) = `No)
+      Sys_unix.ls_dir absolute_path
+      |> List.for_all ~f:(fun path -> Sys_unix.is_directory (absolute_path ^/ path) = `No)
     in
     if is_leaf_directory absolute_path then
       match parse_directory absolute_path with
@@ -178,7 +178,7 @@ let parse_templates ?metasyntax ?(warn_for_missing_file_in_dir = false) paths =
       Continue acc
   in
   List.concat_map paths ~f:(fun path ->
-      if Sys.is_directory path = `Yes then
+      if Sys_unix.is_directory path = `Yes then
         fold_directory path ~sorted:true ~init:[] ~f
       else
         parse_toml ?metasyntax path)
@@ -421,7 +421,7 @@ let parse_metasyntax metasyntax_path =
   match metasyntax_path with
   | None -> Matchers.Metasyntax.default_metasyntax
   | Some metasyntax_path ->
-    match Sys.file_exists metasyntax_path with
+    match Sys_unix.file_exists metasyntax_path with
     | `No | `Unknown ->
       Format.eprintf "Could not open file: %s@." metasyntax_path;
       exit 1
@@ -470,12 +470,12 @@ let emit_errors { input_options; output_options; _ } =
     ; Option.is_some input_options.directory_depth
       && Option.value_exn (input_options.directory_depth) < 0
     , "-depth must be 0 or greater."
-    ; Sys.is_directory input_options.target_directory = `No
+    ; Sys_unix.is_directory input_options.target_directory = `No
     , "Directory specified with -d or -directory is not a directory."
     ; output_options.json_only_diff && not output_options.json_lines
     , "-json-only-diff can only be supplied with -json-lines."
     ; Option.is_some output_options.interactive_review &&
-      (not (String.equal input_options.target_directory (Sys.getcwd ())))
+      (not (String.equal input_options.target_directory (Sys_unix.getcwd ())))
     , "Please remove the -d option and `cd` to the directory where you want to \
        review from. The -review, -editor, or -default-no options should only be run \
        at the root directory of the project files to patch."
@@ -483,11 +483,11 @@ let emit_errors { input_options; output_options; _ } =
          match input_options.templates with
          | Some inputs ->
            List.find_map inputs ~f:(fun input ->
-               if Sys.is_file input = `Yes then
+               if Sys_unix.is_file input = `Yes then
                  (match Toml.Parser.from_filename input with
                   | `Error (s, _) -> Some s
                   | _ -> None)
-               else if not (Sys.is_directory input = `Yes) then
+               else if not (Sys_unix.is_directory input = `Yes) then
                  Some (Format.sprintf "Directory %S specified with -templates is not a directory." input)
                else
                  None)
@@ -599,7 +599,7 @@ let filter_zip_entries file_filters exclude_directory_prefix exclude_file_prefix
 
 let syntax custom_matcher_path =
   match
-    Sys.file_exists custom_matcher_path with
+    Sys_unix.file_exists custom_matcher_path with
   | `No | `Unknown ->
     Format.eprintf "Could not open file: %s@." custom_matcher_path;
     exit 1
@@ -783,7 +783,7 @@ let create
     | Directory ->
       let target_directory =
         if target_directory = "." then
-          Filename.realpath target_directory
+          Filename_unix.realpath target_directory
         else
           target_directory
       in
diff --git a/lib/app/configuration/dune b/lib/app/configuration/dune
index e0f9748..e417cfe 100644
--- a/lib/app/configuration/dune
+++ b/lib/app/configuration/dune
@@ -1,6 +1,21 @@
 (library
-  (name configuration)
-  (public_name comby.configuration)
-  (instrumentation (backend bisect_ppx))
-  (preprocess (pps ppx_deriving.show ppx_sexp_conv ppx_sexp_message ppx_deriving_yojson))
-  (libraries comby-kernel comby-semantic comby.patdiff comby.camlzip core yojson ppx_deriving_yojson toml lwt lwt.unix tar tar-unix))
+ (name configuration)
+ (public_name comby.configuration)
+ (instrumentation
+  (backend bisect_ppx))
+ (preprocess
+  (pps ppx_deriving.show ppx_sexp_conv ppx_sexp_message ppx_deriving_yojson))
+ (libraries
+  comby-kernel
+  comby-semantic
+  comby.patdiff
+  comby.camlzip
+  core
+  core_unix.sys_unix
+  yojson
+  ppx_deriving_yojson
+  toml
+  lwt
+  lwt.unix
+  tar
+  tar-unix))
diff --git a/lib/app/configuration/external_semantic.ml b/lib/app/configuration/external_semantic.ml
index bdc7051..ac69b1b 100644
--- a/lib/app/configuration/external_semantic.ml
+++ b/lib/app/configuration/external_semantic.ml
@@ -2,13 +2,10 @@ open Core_kernel
 
 open Comby_semantic
 
-let debug =
-  match Sys.getenv "DEBUG_COMBY" with
-  | exception Not_found -> false
-  | _ -> true
+let debug = Sys.getenv "DEBUG_COMBY" |> Option.is_some
 
 let lsif_hover ~name:_ ~filepath ~line ~column =
-  String.chop_prefix_if_exists filepath ~prefix:(Sys.getcwd ()) |> fun filepath_relative_root ->
+  String.chop_prefix_if_exists filepath ~prefix:(Sys_unix.getcwd ()) |> fun filepath_relative_root ->
   if debug then Format.printf "File relative root: %s@." filepath;
   if debug then Format.printf "Querying type at %d::%d@." line column;
   let context =
diff --git a/lib/app/dune b/lib/app/dune
index 2ed553c..a91f826 100644
--- a/lib/app/dune
+++ b/lib/app/dune
@@ -1,9 +1,8 @@
 (library
-  (name comby)
-  (public_name comby)
-  (instrumentation (backend bisect_ppx))
-  (preprocess (pps ppx_deriving.show ppx_deriving.eq ppx_sexp_conv))
-  (libraries 
-   core 
-   comby-kernel
-   comby.pipeline))
+ (name comby)
+ (public_name comby)
+ (instrumentation
+  (backend bisect_ppx))
+ (preprocess
+  (pps ppx_deriving.show ppx_deriving.eq ppx_sexp_conv))
+ (libraries core comby-kernel comby.pipeline))
diff --git a/lib/app/interactive/dune b/lib/app/interactive/dune
index 815aff5..63c1757 100644
--- a/lib/app/interactive/dune
+++ b/lib/app/interactive/dune
@@ -1,5 +1,12 @@
 (library
-  (name interactive)
-  (public_name comby.interactive)
-  (preprocess (pps ppx_sexp_conv))
-  (libraries comby-kernel comby.configuration core shell.filename_extended lwt lwt.unix))
+ (name interactive)
+ (public_name comby.interactive)
+ (preprocess
+  (pps ppx_sexp_conv))
+ (libraries
+  comby-kernel
+  comby.configuration
+  core
+  shell.filename_extended
+  lwt
+  lwt.unix))
diff --git a/lib/app/interactive/interactive.ml b/lib/app/interactive/interactive.ml
index d4bf200..b27105a 100644
--- a/lib/app/interactive/interactive.ml
+++ b/lib/app/interactive/interactive.ml
@@ -1,5 +1,6 @@
 open Core
 open Lwt
+module Unix = Core_unix
 
 open Configuration
 
@@ -37,6 +38,7 @@ module Diff = struct
           ~big_enough:line_big_enough
           ~prev
           ~next
+          ()
       | Some prog ->
         let compare x y =
           let cmd = sprintf "%s %S %S" prog x y in
@@ -52,7 +54,7 @@ module Diff = struct
             let compare = compare
           end)
         in
-        P.get_hunks ~transform ~context ~big_enough:line_big_enough ~prev ~next
+        P.get_hunks ~transform ~context ~big_enough:line_big_enough ~prev ~next ()
     in
     match float_tolerance with
     | None -> hunks
diff --git a/lib/app/pipeline/dune b/lib/app/pipeline/dune
index 3369b9e..e6ec880 100644
--- a/lib/app/pipeline/dune
+++ b/lib/app/pipeline/dune
@@ -1,11 +1,23 @@
 (library
-  (name pipeline)
-  (public_name comby.pipeline)
-  (instrumentation (backend bisect_ppx))
-  (preprocess (pps ppx_sexp_conv ppx_deriving_yojson))
-  (libraries comby-kernel comby.statistics comby.configuration comby.interactive comby.camlzip core core.uuid yojson ppx_deriving_yojson parany
-    (select parallel_hack.ml from
-      (hack_parallel -> parallel_hack.available.ml)
-      (!hack_parallel -> parallel_hack.parany_fallback.ml)) 
-  ))
-
+ (name pipeline)
+ (public_name comby.pipeline)
+ (instrumentation
+  (backend bisect_ppx))
+ (preprocess
+  (pps ppx_sexp_conv ppx_deriving_yojson))
+ (libraries
+  comby-kernel
+  comby.statistics
+  comby.configuration
+  comby.interactive
+  comby.camlzip
+  core
+  core_unix.uuid
+  yojson
+  ppx_deriving_yojson
+  parany
+  (select
+   parallel_hack.ml
+   from
+   (hack_parallel -> parallel_hack.available.ml)
+   (!hack_parallel -> parallel_hack.parany_fallback.ml))))
diff --git a/lib/app/pipeline/parallel_hack.available.ml b/lib/app/pipeline/parallel_hack.available.ml
index a901eea..ad33070 100644
--- a/lib/app/pipeline/parallel_hack.available.ml
+++ b/lib/app/pipeline/parallel_hack.available.ml
@@ -1,4 +1,5 @@
 open Core
+module Unix = Core_unix
 
 open Hack_parallel
 
diff --git a/lib/app/statistics/dune b/lib/app/statistics/dune
index b14d5b1..12aff7f 100644
--- a/lib/app/statistics/dune
+++ b/lib/app/statistics/dune
@@ -1,6 +1,8 @@
 (library
-  (name statistics)
-  (public_name comby.statistics)
-  (instrumentation (backend bisect_ppx))
-  (preprocess (pps ppx_deriving_yojson))
-  (libraries yojson ppx_deriving_yojson ppx_deriving_yojson.runtime))
+ (name statistics)
+ (public_name comby.statistics)
+ (instrumentation
+  (backend bisect_ppx))
+ (preprocess
+  (pps ppx_deriving_yojson))
+ (libraries yojson ppx_deriving_yojson ppx_deriving_yojson.runtime))
diff --git a/lib/app/vendored/camlzip/dune b/lib/app/vendored/camlzip/dune
index 56ea8ff..1c67be1 100644
--- a/lib/app/vendored/camlzip/dune
+++ b/lib/app/vendored/camlzip/dune
@@ -7,7 +7,9 @@
  ; as long as the unix parts are not needed, but I want it to 
  ; compile executables for tests
  (libraries unix)
- (foreign_stubs (language c) (names zlibstubs))
+ (foreign_stubs
+  (language c)
+  (names zlibstubs))
  (c_library_flags
   (:include c_flags.sexp)
   (:include c_library_flags.sexp)))
@@ -21,7 +23,9 @@
 
 (env
  (dev
-  (flags (:standard -w A-3-4-27-29-32-34-35-39-40-41-42-44-45-48-49-50-57-60)))
+  (flags
+   (:standard -w A-3-4-27-29-32-34-35-39-40-41-42-44-45-48-49-50-57-60)))
  (release
-  (flags (:standard -w A-3-4-27-29-32-34-35-39-40-41-42-44-45-48-49-50-57-60))
- (ocamlopt_flags (-O3))))
+  (flags
+   (:standard -w A-3-4-27-29-32-34-35-39-40-41-42-44-45-48-49-50-57-60))
+  (ocamlopt_flags (-O3))))
diff --git a/lib/app/vendored/patdiff/kernel/src/dune b/lib/app/vendored/patdiff/kernel/src/dune
index 7a6353d..b79cba2 100644
--- a/lib/app/vendored/patdiff/kernel/src/dune
+++ b/lib/app/vendored/patdiff/kernel/src/dune
@@ -1,3 +1,6 @@
-(library (name patdiff_kernel) (public_name comby.patdiff_kernel)
+(library
+ (name patdiff_kernel)
+ (public_name comby.patdiff_kernel)
  (libraries core_kernel.composition_infix core_kernel patience_diff re)
- (preprocess (pps ppx_jane)))
+ (preprocess
+  (pps ppx_jane)))
diff --git a/lib/app/vendored/patdiff/kernel/src/patdiff_core.ml b/lib/app/vendored/patdiff/kernel/src/patdiff_core.ml
index 4f53a0b..88ee0e3 100644
--- a/lib/app/vendored/patdiff/kernel/src/patdiff_core.ml
+++ b/lib/app/vendored/patdiff/kernel/src/patdiff_core.ml
@@ -138,6 +138,7 @@ module Make (Output_impls : Output_impls) = struct
       ~big_enough:line_big_enough
       ~prev
       ~next
+      ()
   ;;
 
   type word_or_newline =
@@ -345,6 +346,7 @@ module Make (Output_impls : Output_impls) = struct
       ~big_enough:word_big_enough
       ~prev:prev_pieces
       ~next:next_pieces
+      ()
   ;;
 
   let ranges_are_just_whitespace (ranges : _ Patience_diff.Range.t list) =
diff --git a/lib/app/vendored/patdiff/lib/src/compare_core.ml b/lib/app/vendored/patdiff/lib/src/compare_core.ml
index fafb201..8b40d09 100644
--- a/lib/app/vendored/patdiff/lib/src/compare_core.ml
+++ b/lib/app/vendored/patdiff/lib/src/compare_core.ml
@@ -1,5 +1,6 @@
 open! Core
 open! Import
+module Unix = Core_unix
 
 let lines_of_contents contents =
   let lines = Array.of_list (String.split_lines contents) in
@@ -100,6 +101,7 @@ let compare_lines (config : Configuration.t) ?prev_diff ?next_diff ~prev ~next (
         ~big_enough:line_big_enough
         ~prev
         ~next
+        ()
     | Some prog ->
       let compare x y =
         let cmd = sprintf "%s %S %S" prog x y in
@@ -116,7 +118,7 @@ let compare_lines (config : Configuration.t) ?prev_diff ?next_diff ~prev ~next (
           let compare = compare
         end)
       in
-      P.get_hunks ~transform ~context ~big_enough:line_big_enough ~prev ~next
+      P.get_hunks ~transform ~context ~big_enough:line_big_enough ~prev ~next ()
   in
   let hunks =
     match config.float_tolerance with
@@ -361,7 +363,7 @@ let rec diff_dirs_internal (config : Configuration.t) ~prev_dir ~next_dir ~file_
       | None -> Fn.const true
       | Some file_filter -> file_filter
     in
-    Sys.ls_dir (File_name.real_name_exn dir)
+    Sys_unix.ls_dir (File_name.real_name_exn dir)
     |> List.filter ~f:(fun x ->
       let x = File_name.real_name_exn dir ^/ x in
       match Unix.stat x with
diff --git a/lib/app/vendored/patdiff/lib/src/compare_core.mli b/lib/app/vendored/patdiff/lib/src/compare_core.mli
index e919512..caa8dcb 100644
--- a/lib/app/vendored/patdiff/lib/src/compare_core.mli
+++ b/lib/app/vendored/patdiff/lib/src/compare_core.mli
@@ -1,5 +1,6 @@
 open! Core
 open! Import
+module Unix = Core_unix
 
 val diff_files
   :  Configuration.t
diff --git a/lib/app/vendored/patdiff/lib/src/configuration.ml b/lib/app/vendored/patdiff/lib/src/configuration.ml
index 6879daa..7d59706 100644
--- a/lib/app/vendored/patdiff/lib/src/configuration.ml
+++ b/lib/app/vendored/patdiff/lib/src/configuration.ml
@@ -481,7 +481,7 @@ let rec load_exn' ~set config_file =
        | Error _another_exn -> raise exn
        | Ok c ->
          (let new_file = config_file ^ ".new" in
-          match Sys.file_exists new_file with
+          match Sys_unix.file_exists new_file with
           | `Yes | `Unknown -> ()
           | `No ->
             (try Sexp.save_hum new_file (On_disk.V1.sexp_of_t c) with
@@ -564,7 +564,7 @@ let get_config ?filename () =
       (* ~/.patdiff exists *)
       Option.bind (Sys.getenv "HOME") ~f:(fun home ->
         let f = home ^/ ".patdiff" in
-        match Sys.file_exists f with
+        match Sys_unix.file_exists f with
         | `Yes -> Some f
         | `No | `Unknown -> None)
   in
diff --git a/lib/app/vendored/patdiff/lib/src/dune b/lib/app/vendored/patdiff/lib/src/dune
index 007acad..b6a0f80 100644
--- a/lib/app/vendored/patdiff/lib/src/dune
+++ b/lib/app/vendored/patdiff/lib/src/dune
@@ -1,4 +1,13 @@
-(library (name patdiff) (public_name comby.patdiff)
- (libraries core_kernel.composition_infix core core.linux_ext comby.patdiff_kernel
+(library
+ (name patdiff)
+ (public_name comby.patdiff)
+ (libraries
+  core_kernel.composition_infix
+  core
+  core_unix
+  core_unix.linux_ext
+  core_unix.sys_unix
+  comby.patdiff_kernel
   patience_diff)
- (preprocess (pps ppx_jane)))
+ (preprocess
+  (pps ppx_jane)))
diff --git a/lib/app/vendored/patdiff/lib/src/html_output.ml b/lib/app/vendored/patdiff/lib/src/html_output.ml
index 3d08f91..93ae8af 100644
--- a/lib/app/vendored/patdiff/lib/src/html_output.ml
+++ b/lib/app/vendored/patdiff/lib/src/html_output.ml
@@ -1,5 +1,6 @@
 open! Core
 open! Import
+module Unix = Core_unix
 
 include Patdiff_kernel.Html_output.Private.Make (struct
     let mtime file =
diff --git a/lib/kernel/dune b/lib/kernel/dune
index 0961dad..07a929b 100644
--- a/lib/kernel/dune
+++ b/lib/kernel/dune
@@ -1,10 +1,12 @@
 (library
-  (name comby_kernel)
-  (public_name comby-kernel)
-  (instrumentation (backend bisect_ppx))
-  (preprocess (pps ppx_deriving.show ppx_deriving.eq ppx_sexp_conv))
-  (libraries 
-   core_kernel
-   comby-kernel.match
-   comby-kernel.matchers
-   comby-kernel.replacement))
+ (name comby_kernel)
+ (public_name comby-kernel)
+ (instrumentation
+  (backend bisect_ppx))
+ (preprocess
+  (pps ppx_deriving.show ppx_deriving.eq ppx_sexp_conv))
+ (libraries
+  core_kernel
+  comby-kernel.match
+  comby-kernel.matchers
+  comby-kernel.replacement))
diff --git a/lib/kernel/match/dune b/lib/kernel/match/dune
index 03b120a..4d48b61 100644
--- a/lib/kernel/match/dune
+++ b/lib/kernel/match/dune
@@ -1,6 +1,12 @@
 (library
-  (name match)
-  (public_name comby-kernel.match)
-  (instrumentation (backend bisect_ppx))
-  (preprocess (pps ppx_deriving.eq ppx_sexp_conv ppx_deriving_yojson))
-  (libraries core_kernel yojson ppx_deriving_yojson ppx_deriving_yojson.runtime))
+ (name match)
+ (public_name comby-kernel.match)
+ (instrumentation
+  (backend bisect_ppx))
+ (preprocess
+  (pps ppx_deriving.eq ppx_sexp_conv ppx_deriving_yojson))
+ (libraries
+  core_kernel
+  yojson
+  ppx_deriving_yojson
+  ppx_deriving_yojson.runtime))
diff --git a/lib/kernel/matchers/alpha.ml b/lib/kernel/matchers/alpha.ml
index e31094d..01adb52 100644
--- a/lib/kernel/matchers/alpha.ml
+++ b/lib/kernel/matchers/alpha.ml
@@ -13,20 +13,11 @@ module R = MakeRegexp(Regexp)
 let configuration_ref = ref (Configuration.create ())
 let weaken_delimiter_hole_matching = false
 
-let debug =
-  match Sys.getenv "DEBUG_COMBY" with
-  | exception Not_found -> false
-  | _ -> true
+let debug = Sys.getenv "DEBUG_COMBY" |> Option.is_some
 
-let debug_hole =
-  match Sys.getenv "DEBUG_COMBY_HOLE" with
-  | exception Not_found -> false
-  | _ -> true
+let debug_hole = Sys.getenv "DEBUG_COMBY_HOLE" |> Option.is_some
 
-let debug_position =
-  match Sys.getenv "DEBUG_COMBY_POS" with
-  | exception Not_found -> false
-  | _ -> true
+let debug_position = Sys.getenv "DEBUG_COMBY_POS" |> Option.is_some
 
 let f _ = return Types.Unit
 
@@ -147,7 +138,7 @@ module Make (Lang : Types.Language.S) (Meta : Types.Metasyntax.S) (Ext : Types.E
         ]
       >>= fun _ -> f Types.Unit
 
-    let sequence_chain (plist : ('c, Match.t) parser sexp_list) : ('c, Match.t) parser =
+    let sequence_chain (plist : ('c, Match.t) parser list) : ('c, Match.t) parser =
       List.fold plist ~init:(return Types.Unit) ~f:(>>)
 
     let with_debug_matcher s tag =
diff --git a/lib/kernel/matchers/dune b/lib/kernel/matchers/dune
index 12ed326..4625458 100644
--- a/lib/kernel/matchers/dune
+++ b/lib/kernel/matchers/dune
@@ -1,6 +1,18 @@
 (library
-  (name matchers)
-  (public_name comby-kernel.matchers)
-  (instrumentation (backend bisect_ppx))
-  (preprocess (pps ppx_here ppx_sexp_conv ppx_sexp_message ppx_deriving_yojson))
-  (libraries comby-kernel.replacement comby-kernel.parsers comby-kernel.match comby-kernel.vangstrom core_kernel mparser mparser-pcre re yojson ppx_deriving_yojson))
+ (name matchers)
+ (public_name comby-kernel.matchers)
+ (instrumentation
+  (backend bisect_ppx))
+ (preprocess
+  (pps ppx_here ppx_sexp_conv ppx_sexp_message ppx_deriving_yojson))
+ (libraries
+  comby-kernel.replacement
+  comby-kernel.parsers
+  comby-kernel.match
+  comby-kernel.vangstrom
+  core_kernel
+  mparser
+  mparser-pcre
+  re
+  yojson
+  ppx_deriving_yojson))
diff --git a/lib/kernel/matchers/evaluate.ml b/lib/kernel/matchers/evaluate.ml
index 9ea71a0..288f79a 100644
--- a/lib/kernel/matchers/evaluate.ml
+++ b/lib/kernel/matchers/evaluate.ml
@@ -3,10 +3,7 @@ open Core_kernel
 open Match
 open Types.Ast
 
-let debug =
-  match Sys.getenv "DEBUG_COMBY" with
-  | exception Not_found -> false
-  | _ -> true
+let debug = Sys.getenv "DEBUG_COMBY" |> Option.is_some
 
 type result = bool * Match.environment option
 
diff --git a/lib/kernel/matchers/omega.ml b/lib/kernel/matchers/omega.ml
index eeec516..1eb3ccc 100644
--- a/lib/kernel/matchers/omega.ml
+++ b/lib/kernel/matchers/omega.ml
@@ -32,15 +32,9 @@ let push_source_ref : string ref = ref ""
 
 let filepath_ref : string option ref = ref None
 
-let debug =
-  match Sys.getenv "DEBUG_COMBY" with
-  | exception Not_found -> false
-  | _ -> true
+let debug = Sys.getenv "DEBUG_COMBY" |> Option.is_some
 
-let rewrite =
-  match Sys.getenv "REWRITE" with
-  | exception Not_found -> false
-  | _ -> true
+let rewrite = Sys.getenv "REWRITE" |> Option.is_some
 
 let actual = Buffer.create 10
 
diff --git a/lib/kernel/matchers/preprocess.ml b/lib/kernel/matchers/preprocess.ml
index 84f3ed0..b6d10e7 100644
--- a/lib/kernel/matchers/preprocess.ml
+++ b/lib/kernel/matchers/preprocess.ml
@@ -1,9 +1,6 @@
 open Core_kernel
 
-let debug =
-  match Sys.getenv "DEBUG_COMBY" with
-  | exception Not_found -> false
-  | _ -> true
+let debug = Sys.getenv "DEBUG_COMBY" |> Option.is_some
 
 let append_rule (module Parser : Types.Rule.S) rule parent_rule =
   let open Option in
diff --git a/lib/kernel/matchers/regexp.ml b/lib/kernel/matchers/regexp.ml
index ef0bd59..906820b 100644
--- a/lib/kernel/matchers/regexp.ml
+++ b/lib/kernel/matchers/regexp.ml
@@ -3,7 +3,7 @@ open Vangstrom
 let debug =
   match Sys.getenv "DEBUG_COMBY" with
   | exception Not_found -> false
-  | _ -> true
+  | (_ : string) -> true
 
 module type Regexp_engine_intf = sig
   type t
diff --git a/lib/kernel/matchers/rewrite.ml b/lib/kernel/matchers/rewrite.ml
index 32c4740..2fc28db 100644
--- a/lib/kernel/matchers/rewrite.ml
+++ b/lib/kernel/matchers/rewrite.ml
@@ -4,10 +4,7 @@ open Core_kernel
 open Match
 open Replacement
 
-let debug =
-  match Sys.getenv "DEBUG_COMBY" with
-  | exception Not_found -> false
-  | _ -> true
+let debug = Sys.getenv "DEBUG_COMBY" |> Option.is_some
 
 let counter =
   let uuid_for_id_counter = ref 0 in
diff --git a/lib/kernel/matchers/template.ml b/lib/kernel/matchers/template.ml
index 423a07f..136236c 100644
--- a/lib/kernel/matchers/template.ml
+++ b/lib/kernel/matchers/template.ml
@@ -4,10 +4,7 @@ open Core_kernel
 open Match
 open Types.Template
 
-let debug =
-  match Sys.getenv "DEBUG_COMBY" with
-  | exception Not_found -> false
-  | _ -> true
+let debug = Sys.getenv "DEBUG_COMBY" |> Option.is_some
 
 module Make (Metasyntax : Types.Metasyntax.S) (External : Types.External.S) : Types.Template.S = struct
 
diff --git a/lib/kernel/parsers/dune b/lib/kernel/parsers/dune
index 28b020c..0cc1fa5 100644
--- a/lib/kernel/parsers/dune
+++ b/lib/kernel/parsers/dune
@@ -1,6 +1,8 @@
 (library
-  (name parsers)
-  (public_name comby-kernel.parsers)
-  (instrumentation (backend bisect_ppx))
-  (preprocess (pps ppx_sexp_conv))
-  (libraries core_kernel comby-kernel.vangstrom mparser))
+ (name parsers)
+ (public_name comby-kernel.parsers)
+ (instrumentation
+  (backend bisect_ppx))
+ (preprocess
+  (pps ppx_sexp_conv))
+ (libraries core_kernel comby-kernel.vangstrom mparser))
diff --git a/lib/kernel/replacement/dune b/lib/kernel/replacement/dune
index 3e62de6..485b716 100644
--- a/lib/kernel/replacement/dune
+++ b/lib/kernel/replacement/dune
@@ -1,6 +1,13 @@
 (library
-  (name replacement)
-  (public_name comby-kernel.replacement)
-  (instrumentation (backend bisect_ppx))
-  (preprocess (pps ppx_deriving_yojson))
-  (libraries comby-kernel.match core_kernel yojson ppx_deriving_yojson ppx_deriving_yojson.runtime))
+ (name replacement)
+ (public_name comby-kernel.replacement)
+ (instrumentation
+  (backend bisect_ppx))
+ (preprocess
+  (pps ppx_deriving_yojson))
+ (libraries
+  comby-kernel.match
+  core_kernel
+  yojson
+  ppx_deriving_yojson
+  ppx_deriving_yojson.runtime))
diff --git a/lib/semantic/dune b/lib/semantic/dune
index 9a244d3..186a2ed 100644
--- a/lib/semantic/dune
+++ b/lib/semantic/dune
@@ -1,11 +1,8 @@
 (library
-   (name comby_semantic)
-   (public_name comby-semantic)
-   (instrumentation (backend bisect_ppx))
-   (preprocess (pps ppx_deriving.show ppx_deriving.eq ppx_sexp_conv))
-   (libraries
-      core_kernel
-      lwt
-      cohttp
-      cohttp-lwt-unix
-      yojson))
+ (name comby_semantic)
+ (public_name comby-semantic)
+ (instrumentation
+  (backend bisect_ppx))
+ (preprocess
+  (pps ppx_deriving.show ppx_deriving.eq ppx_sexp_conv))
+ (libraries core_kernel lwt cohttp cohttp-lwt-unix yojson))
diff --git a/lib/semantic/lsif.ml b/lib/semantic/lsif.ml
index 49747bc..d6b3e19 100644
--- a/lib/semantic/lsif.ml
+++ b/lib/semantic/lsif.ml
@@ -3,10 +3,7 @@ open Lwt
 open Cohttp
 open Cohttp_lwt_unix
 
-let debug =
-  match Sys.getenv "DEBUG_COMBY" with
-  | exception Not_found -> false
-  | _ -> true
+let debug = Sys.getenv "DEBUG_COMBY" |> Option.is_some
 
 module Formatting = struct
   type t =
diff --git a/src/dune b/src/dune
index 444a5a3..f006195 100644
--- a/src/dune
+++ b/src/dune
@@ -1,10 +1,17 @@
 (executables
- (libraries comby core ppx_deriving_yojson ppx_deriving_yojson.runtime
-    (select if_hack_parallel.ml from
-      (hack_parallel -> if_hack_parallel.available.ml)
-      (!hack_parallel -> if_hack_parallel.unavailable.ml))
- )
- (preprocess (pps ppx_deriving_yojson ppx_let ppx_deriving.show ppx_sexp_conv))
+ (libraries
+  comby
+  core
+  core_unix.command_unix
+  ppx_deriving_yojson
+  ppx_deriving_yojson.runtime
+  (select
+   if_hack_parallel.ml
+   from
+   (hack_parallel -> if_hack_parallel.available.ml)
+   (!hack_parallel -> if_hack_parallel.unavailable.ml)))
+ (preprocess
+  (pps ppx_deriving_yojson ppx_let ppx_deriving.show ppx_sexp_conv))
  (modules main if_hack_parallel)
  (modes byte exe)
  (names main))
@@ -20,4 +27,5 @@
 (install
  (package comby)
  (section bin)
- (files (main.exe as comby)))
+ (files
+  (main.exe as comby)))
diff --git a/src/main.ml b/src/main.ml
index 5cad346..48784d1 100644
--- a/src/main.ml
+++ b/src/main.ml
@@ -1,4 +1,5 @@
 open Core
+module Unix = Core_unix
 open Command.Let_syntax
 
 open Comby_kernel
@@ -47,7 +48,7 @@ let substitute_environment_only_and_exit metasyntax_path anonymous_arguments jso
     match metasyntax_path with
     | None -> Matchers.Metasyntax.default_metasyntax
     | Some metasyntax_path ->
-      match Sys.file_exists metasyntax_path with
+      match Sys_unix.file_exists metasyntax_path with
       | `No | `Unknown ->
         Format.eprintf "Could not open file: %s@." metasyntax_path;
         exit 1
@@ -95,7 +96,7 @@ let base_command_parameters : (unit -> 'result) Command.Param.t =
     and verbose = flag "verbose" no_arg ~doc:(Format.sprintf "Log to %s" verbose_out_file)
     and rule = flag "rule" (optional_with_default "where true" string) ~doc:"rule Apply rules to matches."
     and match_timeout = flag "timeout" (optional_with_default 3 int) ~doc:"seconds Set match timeout on a source. Default: 3 seconds"
-    and target_directory = flag "directory" ~aliases:["d"] (optional_with_default (Sys.getcwd ()) string) ~doc:(Format.sprintf "path Run recursively on files in a directory relative to the root. Default is current directory: %s" @@ Sys.getcwd ())
+    and target_directory = flag "directory" ~aliases:["d"] (optional_with_default (Sys_unix.getcwd ()) string) ~doc:(Format.sprintf "path Run recursively on files in a directory relative to the root. Default is current directory: %s" @@ Sys_unix.getcwd ())
     and directory_depth = flag "depth" (optional int) ~doc:"n Depth to recursively descend into directories"
     and templates = flag "templates" ~aliases:["config"; "configuration"] (optional (Arg_type.comma_separated string)) ~doc:"paths CSV of directories containing templates, or TOML configuration files"
     and file_filters = flag "extensions" ~aliases:["e"; "file-extensions"; "f"] (optional (Arg_type.comma_separated string)) ~doc:"extensions Comma-separated extensions to include, like \".go\" or \".c,.h\". It is just a file suffix, so you can use it to filter file names like \"main.go\". The extension will be used to infer a matcher, unless -custom-matcher or -matcher is specified"
@@ -146,7 +147,7 @@ let base_command_parameters : (unit -> 'result) Command.Param.t =
       | l ->
         List.map l ~f:(fun pattern ->
             if String.contains pattern '/' then
-              match Filename.realpath pattern with
+              match Filename_unix.realpath pattern with
               | exception Unix.Unix_error _ ->
                 Format.eprintf
                   "No such file or directory: %s. Comby interprets \
@@ -203,7 +204,7 @@ let base_command_parameters : (unit -> 'result) Command.Param.t =
     let omega = omega || omega_env in
     let fast_offset_conversion_env = Option.is_some @@ Sys.getenv "FAST_OFFSET_CONVERSION_COMBY" in
     let fast_offset_conversion = fast_offset_conversion_env || fast_offset_conversion in
-    let arch = Unix.Utsname.machine (Core.Unix.uname ()) in
+    let arch = Unix.Utsname.machine (Unix.uname ()) in
     let compute_mode = match sequential, parany, arch with
       | true, _, _ -> `Sequential
       | _, true, _
@@ -301,7 +302,7 @@ let parse_comby_dot_file () =
 
 let () =
   If_hack_parallel.check_entry_point ();
-  Command.run default_command ~version:"1.7.1" ~extend:(fun _ ->
-      match Sys.file_exists ".comby" with
+  Command_unix.run default_command ~version:"1.7.1" ~extend:(fun _ ->
+      match Sys_unix.file_exists ".comby" with
       | `Yes -> parse_comby_dot_file ()
       | _ -> [])
diff --git a/test/alpha/dune b/test/alpha/dune
index d7e5532..020677c 100644
--- a/test/alpha/dune
+++ b/test/alpha/dune
@@ -1,17 +1,14 @@
 (library
  (name alpha_test_integration)
  (package comby)
- (modules
-  test_special_matcher_cases
-  test_substring_disabled)
+ (modules test_special_matcher_cases test_substring_disabled)
  (inline_tests)
- (preprocess (pps ppx_expect ppx_sexp_message ppx_deriving_yojson))
- (libraries
-  comby
-  cohttp-lwt-unix
-  core
-  camlzip))
+ (preprocess
+  (pps ppx_expect ppx_sexp_message ppx_deriving_yojson))
+ (libraries comby cohttp-lwt-unix core camlzip))
 
 (alias
-(name runtest)
-(deps (source_tree example) (source_tree example/src/.ignore-me)))
+ (name runtest)
+ (deps
+  (source_tree example)
+  (source_tree example/src/.ignore-me)))
diff --git a/test/common/dune b/test/common/dune
index aa83b0c..3793242 100644
--- a/test/common/dune
+++ b/test/common/dune
@@ -34,16 +34,14 @@
   test_regex_holes
   test_template_constraints
   test_custom_metasyntax
-  test_rewrite_attributes
-  )
+  test_rewrite_attributes)
  (inline_tests)
- (preprocess (pps ppx_expect ppx_sexp_message ppx_deriving_yojson))
- (libraries
-  comby
-  cohttp-lwt-unix
-  core
-  camlzip))
+ (preprocess
+  (pps ppx_expect ppx_sexp_message ppx_deriving_yojson))
+ (libraries comby cohttp-lwt-unix core camlzip))
 
 (alias
-(name runtest)
-(deps (source_tree example) (source_tree example/src/.ignore-me)))
+ (name runtest)
+ (deps
+  (source_tree example)
+  (source_tree example/src/.ignore-me)))
diff --git a/test/common/test_cli.ml b/test/common/test_cli.ml
index 3606367..d5d0c0b 100644
--- a/test/common/test_cli.ml
+++ b/test/common/test_cli.ml
@@ -1,7 +1,10 @@
 open Core
 open Camlzip
 
+module Filename = Filename_unix
+module Sys = Sys_unix
 module Time = Core_kernel.Time_ns.Span
+module Unix = Core_unix
 
 let binary_path = "../../../../comby"
 
diff --git a/test/common/test_cli_helper.ml b/test/common/test_cli_helper.ml
index 5791ee6..18372ae 100644
--- a/test/common/test_cli_helper.ml
+++ b/test/common/test_cli_helper.ml
@@ -1,6 +1,7 @@
 open Core
 
 module Time = Core_kernel.Time_ns.Span
+module Unix = Core_unix
 
 let binary_path = "../../../../comby"
 
diff --git a/test/omega/dune b/test/omega/dune
index 3b31a7e..bf68dcb 100644
--- a/test/omega/dune
+++ b/test/omega/dune
@@ -2,20 +2,19 @@
  (name omega_test_integration)
  (package comby)
  (modules
-;
-; TODO
-;
+  ;
+  ; TODO
+  ;
   test_optional_holes
   test_special_matcher_cases
   test_substring_disabled)
  (inline_tests)
- (preprocess (pps ppx_expect ppx_sexp_message ppx_deriving_yojson))
- (libraries
-  comby
-  cohttp-lwt-unix
-  core
-  camlzip))
+ (preprocess
+  (pps ppx_expect ppx_sexp_message ppx_deriving_yojson))
+ (libraries comby cohttp-lwt-unix core camlzip))
 
 (alias
-(name runtest)
-(deps (source_tree example) (source_tree example/src/.ignore-me)))
+ (name runtest)
+ (deps
+  (source_tree example)
+  (source_tree example/src/.ignore-me)))