From 29af2fd406faf7ab845374d1d0b95c6e529d73d0 Mon Sep 17 00:00:00 2001
From: Kate <kit-ty-kate@outlook.com>
Date: Wed, 26 Mar 2025 16:26:48 +0000
Subject: [PATCH 1/4] Replace the use of GNU Patch by the OCaml patch library

---
 .github/workflows/ci.ml          |   4 +-
 .github/workflows/main.yml       |   4 +-
 configure                        |  26 +++++++
 configure.ac                     |   2 +
 master_changes.md                |  10 +++
 opam-core.opam                   |   1 +
 opam-repository.opam             |   1 +
 src/client/opamAction.ml         | 116 +++++++++++++++----------------
 src/client/opamAction.mli        |   2 +-
 src/client/opamInitDefaults.ml   |   8 ---
 src/core/dune                    |   2 +-
 src/core/opamFilename.ml         |   5 +-
 src/core/opamFilename.mli        |   8 ++-
 src/core/opamSystem.ml           | 106 ++++++++++++++++++----------
 src/core/opamSystem.mli          |   8 ++-
 src/repository/opamRepository.ml |  10 +--
 src_ext/Makefile                 |   5 +-
 src_ext/Makefile.sources         |   3 +
 tests/reftests/repository.test   |  16 ++---
 19 files changed, 202 insertions(+), 135 deletions(-)

diff --git a/.github/workflows/ci.ml b/.github/workflows/ci.ml
index 2fc71589177..c2e22d86095 100644
--- a/.github/workflows/ci.ml
+++ b/.github/workflows/ci.ml
@@ -527,8 +527,8 @@ let main oc : unit =
     ("OPAM12CACHE", "~/.cache/opam1.2/cache");
     (* These should be identical to the values in appveyor.yml *)
     ("OPAM_REPO", "https://github.com/ocaml/opam-repository.git");
-    ("OPAM_TEST_REPO_SHA", "67e940587b8aca227f511e1943bcd31eabe6b1db");
-    ("OPAM_REPO_SHA", "67e940587b8aca227f511e1943bcd31eabe6b1db");
+    ("OPAM_TEST_REPO_SHA", "0c42e982f4cf97fc698132fb2a16b49524a26ab3");
+    ("OPAM_REPO_SHA", "0c42e982f4cf97fc698132fb2a16b49524a26ab3");
     ("SOLVER", "");
     (* Cygwin configuration *)
     ("CYGWIN_MIRROR", "http://mirrors.kernel.org/sourceware/cygwin/");
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 4b4631d2d2a..ce1c2187db7 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -26,8 +26,8 @@ env:
   OPAMBSROOT: ~/.cache/.opam.cached
   OPAM12CACHE: ~/.cache/opam1.2/cache
   OPAM_REPO: https://github.com/ocaml/opam-repository.git
-  OPAM_TEST_REPO_SHA: 67e940587b8aca227f511e1943bcd31eabe6b1db
-  OPAM_REPO_SHA: 67e940587b8aca227f511e1943bcd31eabe6b1db
+  OPAM_TEST_REPO_SHA: 0c42e982f4cf97fc698132fb2a16b49524a26ab3
+  OPAM_REPO_SHA: 0c42e982f4cf97fc698132fb2a16b49524a26ab3
   SOLVER:
   CYGWIN_MIRROR: http://mirrors.kernel.org/sourceware/cygwin/
   CYGWIN_ROOT: D:\cygwin
diff --git a/configure b/configure
index 10a0cd26ce9..5765227408c 100755
--- a/configure
+++ b/configure
@@ -622,6 +622,7 @@ ac_ct_CXX
 CXXFLAGS
 CXX
 OCAML_PKG_mccs
+OCAML_PKG_patch
 OCAML_PKG_swhid_core
 OCAML_PKG_sha
 OCAML_PKG_uutf
@@ -6521,6 +6522,30 @@ printf "%s\n" "not found" >&6; }
 
 
 
+  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for OCaml findlib package patch" >&5
+printf %s "checking for OCaml findlib package patch... " >&6; }
+
+  unset found
+  unset pkg
+  found=no
+  for pkg in patch  ; do
+    if $OCAMLFIND query $pkg >/dev/null 2>/dev/null; then
+      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: found" >&5
+printf "%s\n" "found" >&6; }
+      OCAML_PKG_patch=$pkg
+      found=yes
+      break
+    fi
+  done
+  if test "$found" = "no" ; then
+    { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: not found" >&5
+printf "%s\n" "not found" >&6; }
+    OCAML_PKG_patch=no
+  fi
+
+
+
+
 # Optional dependencies
 
   { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for OCaml findlib package mccs 1.1+17 or later" >&5
@@ -7047,6 +7072,7 @@ if test "x${enable_checks}" != "xno" && {
        test "x$OCAML_PKG_uutf" = "xno" ||
        test "x$OCAML_PKG_sha" = "xno" ||
        test "x$OCAML_PKG_swhid_core" = "xno" ||
+       test "x$OCAML_PKG_patch" = "xno" ||
        test "x$OCAML_PKG_mccs$MCCS_ENABLED" = "xnotrue";}
 then :
 
diff --git a/configure.ac b/configure.ac
index 919416bd320..22d13216573 100644
--- a/configure.ac
+++ b/configure.ac
@@ -366,6 +366,7 @@ AC_CHECK_OCAML_PKG([jsonm])
 AC_CHECK_OCAML_PKG([uutf])
 AC_CHECK_OCAML_PKG([sha])
 AC_CHECK_OCAML_PKG([swhid_core])
+AC_CHECK_OCAML_PKG([patch])
 
 # Optional dependencies
 AC_CHECK_OCAML_PKG_AT_LEAST([mccs],[1.1+17])
@@ -414,6 +415,7 @@ AS_IF([test "x${enable_checks}" != "xno" && {
        test "x$OCAML_PKG_uutf" = "xno" ||
        test "x$OCAML_PKG_sha" = "xno" ||
        test "x$OCAML_PKG_swhid_core" = "xno" ||
+       test "x$OCAML_PKG_patch" = "xno" ||
        test "x$OCAML_PKG_mccs$MCCS_ENABLED" = "xnotrue";}],[
   AS_IF([test "x${with_vendored_deps}" != "xyes"],[
     AC_MSG_ERROR([Dependencies missing. Use --with-vendored-deps or --disable-checks])
diff --git a/master_changes.md b/master_changes.md
index ea555e4fa3e..60a7c3388eb 100644
--- a/master_changes.md
+++ b/master_changes.md
@@ -29,6 +29,9 @@ users)
 ## Install
 
 ## Build (package)
+  * Patches are now applied using the `patch` OCaml library instead of GNU Patch [#5892 @kit-ty-kate - fix #6019 #6052]
+  * ✘ Patches: Context diffs are not supported anymore, only Unified diffs are (including its git extensions) [#5892 @kit-ty-kate]
+  * ✘ Patches: Stop support of file permission changes via git extension to the unified diff specification [#5892 @kit-ty-kate - fix #3782]
 
 ## Remove
 
@@ -65,6 +68,7 @@ users)
   * [BUG] Do not show the not-up-to-date message with packages tagged with avoid-version [#6273 @kit-ty-kate - fix #6271]
   * [BUG] Fix a regression on `opam upgrade <package>` upgrading unrelated packages [#6373 @AltGr]
   * [BUG] Fix a regression on `opam upgrade --all <uninstalled-pkg>` not upgrading the whole switch [#6373 @kit-ty-kate]
+  * Updates are now applied using the `patch` OCaml library instead of the system GNU Patch [#5892 @kit-ty-kate - fix ocaml/setup-ocaml#933 #6052]
 
 ## Tree
 
@@ -100,6 +104,7 @@ users)
   * Lookup at `gpatch` before `patch` on macOS now that both homebrew and macports expose `gpatch` as `gpatch` since Homebrew/homebrew-core#174687 [#6255 @kit-ty-kate]
   * Relax lookup on OpenBSD to consider all installed packages [#6362 @semarie]
   * Speedup the detection of available system packages with pacman and brew [#6324 @kit-ty-kate]
+  * The system GNU Patch is no longer runtime dependency of opam [#5892 @kit-ty-kate - fix #6052]
 
 ## Format upgrade
 
@@ -226,6 +231,7 @@ users)
 
 # API updates
 ## opam-client
+  * `OpamAction.prepare_package_build`: now returns `exn option` instead of `exn option OpamProcess.job` and no longer calls the system GNU Patch [#5892 @kit-ty-kate]
   * `OpamArg.InvalidCLI`: export exception [#6150 @rjbou]
   * `OpamArg`: export `require_checksums` and `no_checksums`, that are shared with `build_options` [#5563 @rjbou]
   * `OpamArg.hash_kinds`: was added [#5960 @kit-ty-kate]
@@ -254,6 +260,8 @@ users)
 ## opam-core
   * `OpamConsole`: Replace `black` text style (unused and not very readable) by `gray` [#6358 @kit-ty-kate]
   * `OpamConsole.pause`: Ensure the function always prints a newline character at the end [#6376 @kit-ty-kate]
+  * `OpamFilename.patch`: now returns `exn option` instead of `exn option OpamProcess.job` and no longer calls the system GNU Patch [#5892 @kit-ty-kate]
+  * `OpamFilename.patch`: a named-parameter `~allow_unclean` was added [#5892 @kit-ty-kate]
   * `OpamHash.all_kinds`: was added, which returns the list of all possible values of `OpamHash.kind` [#5960 @kit-ty-kate]
   * `OpamStd.List.split`: Improve performance [#6210 @kit-ty-kate]
   * `OpamStd.Option.equal_some`: was added, which tests equality of an option with a value [#6381 @kit-ty-kate]
@@ -265,5 +273,7 @@ users)
   * `OpamStubs.get_stdout_ws_col`: new Unix-only function returning the number of columns of the current terminal window [#6244 @kit-ty-kate]
   * `OpamSystem`: add `is_archive_from_string` that does the same than `is_archive` but without looking at the file, only analysing the string (extension) [#6219 @rjbou]
   * `OpamSystem.remove_dir`: do not fail with an exception when directory is a symbolic link [#6276 @btjorge @rjbou - fix #6275]
+  * `OpamSystem.patch`: now returns `exn option` instead of `exn option OpamProcess.job` and no longer calls the system GNU Patch [#5892 @kit-ty-kate]
+  * `OpamSystem.patch`: a named-parameter `~allow_unclean` was added [#5892 @kit-ty-kate]
   * `OpamParallel.*.{map,reduce,iter}`: Run `Gc.compact` when the main process is waiting for the children processes for the first time [#5396 @kkeundotnet]
   * `OpamSystem`, `OpamFilename`: add `with_tmp_file` and `with_tmp_file_job` function, that create a file name in temporary directory and removes it at the end of the call [#6036 @rjbou]
diff --git a/opam-core.opam b/opam-core.opam
index e9ab6da90b8..d42bc942f91 100644
--- a/opam-core.opam
+++ b/opam-core.opam
@@ -30,6 +30,7 @@ depends: [
   "sha" {>= "1.13"}
   "jsonm"
   "swhid_core"
+  "patch" {>= "3.0.0~alpha1"}
   "uutf"
   (("host-system-mingw" {os = "win32" & os-distribution != "cygwinports"} &
     "conf-mingw-w64-gcc-i686" {os = "win32" & os-distribution != "cygwinports"} &
diff --git a/opam-repository.opam b/opam-repository.opam
index 96505f6887c..3264dd39f0b 100644
--- a/opam-repository.opam
+++ b/opam-repository.opam
@@ -30,5 +30,6 @@ build: [
 depends: [
   "ocaml" {>= "4.08.0"}
   "opam-format" {= version}
+  "patch" {>= "3.0.0~alpha1"}
   "dune" {>= "2.8.0"}
 ]
diff --git a/src/client/opamAction.ml b/src/client/opamAction.ml
index 7781e4aebc5..81a83ee0e75 100644
--- a/src/client/opamAction.ml
+++ b/src/client/opamAction.ml
@@ -367,18 +367,18 @@ let prepare_package_build env opam nv dir =
 
   let apply_patches ?(dryrun=false) () =
     let patch base =
-      if dryrun then Done None else
-        OpamFilename.patch
+      if dryrun then None else
+        OpamFilename.patch ~allow_unclean:true
           (dir // OpamFilename.Base.to_string base) dir
     in
     let rec aux = function
-      | [] -> Done []
+      | [] -> []
       | (patchname,filter)::rest ->
         if OpamFilter.opt_eval_to_bool env filter then
           (print_apply patchname;
-           patch patchname @@+ function
+           match patch patchname with
            | None -> aux rest
-           | Some err -> aux rest @@| fun e -> (patchname, err) :: e)
+           | Some err -> (patchname, err) :: aux rest)
         else aux rest
     in
     aux patches
@@ -390,63 +390,57 @@ let prepare_package_build env opam nv dir =
   in
   if OpamStateConfig.(!r.dryrun) || OpamClientConfig.(!r.fake) then
     (List.iter print_subst (OpamFile.OPAM.substs opam);
-     apply_patches ~dryrun:true ()) @@| fun _ -> None
+     let _ : _ list = apply_patches ~dryrun:true () in
+     None)
   else
-  let subst_errs =
-    OpamFilename.in_dir dir  @@ fun () ->
-    List.fold_left (fun errs f ->
-        try
-          print_subst f;
-          OpamFilter.expand_interpolations_in_file env f;
-          errs
-        with e -> (f, e)::errs)
-      [] subst_patches
-  in
-
-  (* Apply the patches *)
-  let text =
-    OpamProcess.make_command_text (OpamPackage.Name.to_string nv.name) "patch"
-  in
-  OpamProcess.Job.with_text text (apply_patches ())
-  @@+ fun patching_errors ->
-
-  (* Substitute the configuration files. We should be in the right
-     directory to get the correct absolute path for the
-     substitution files (see [OpamFilter.expand_interpolations_in_file] and
-     [OpamFilename.of_basename]. *)
-  let subst_errs =
-    OpamFilename.in_dir dir @@ fun () ->
-    List.fold_left (fun errs f ->
-        try
-          print_subst f;
-          OpamFilter.expand_interpolations_in_file env f;
-          errs
-        with e -> (f, e)::errs)
-      subst_errs subst_others
-  in
-  if patching_errors <> [] || subst_errs <> [] then
-    let msg =
-      (if patching_errors <> [] then
-         Printf.sprintf "These patches didn't apply at %s:\n%s"
-           (OpamFilename.Dir.to_string dir)
-           (OpamStd.Format.itemize
-              (fun (f,err) ->
-                 Printf.sprintf "%s: %s"
-                   (OpamFilename.Base.to_string f) (Printexc.to_string err))
-              patching_errors)
-       else "") ^
-      (if subst_errs <> [] then
-         Printf.sprintf "String expansion failed for these files:\n%s"
-           (OpamStd.Format.itemize
-              (fun (b,err) ->
-                 Printf.sprintf "%s.in: %s" (OpamFilename.Base.to_string b)
-                   (Printexc.to_string err))
-           subst_errs)
-       else "")
+    let subst_errs =
+      OpamFilename.in_dir dir  @@ fun () ->
+      List.fold_left (fun errs f ->
+          try
+            print_subst f;
+            OpamFilter.expand_interpolations_in_file env f;
+            errs
+          with e -> (f, e)::errs)
+        [] subst_patches
     in
-    Done (Some (Failure msg))
-  else
-    Done None
+    let patching_errors = apply_patches () in
+    (* Substitute the configuration files. We should be in the right
+       directory to get the correct absolute path for the
+       substitution files (see [OpamFilter.expand_interpolations_in_file] and
+       [OpamFilename.of_basename]. *)
+    let subst_errs =
+      OpamFilename.in_dir dir @@ fun () ->
+      List.fold_left (fun errs f ->
+          try
+            print_subst f;
+            OpamFilter.expand_interpolations_in_file env f;
+            errs
+          with e -> (f, e)::errs)
+        subst_errs subst_others
+    in
+    if patching_errors <> [] || subst_errs <> [] then
+      let msg =
+        (if patching_errors <> [] then
+           Printf.sprintf "These patches didn't apply at %s:\n%s"
+             (OpamFilename.Dir.to_string dir)
+             (OpamStd.Format.itemize
+                (fun (f,err) ->
+                   Printf.sprintf "%s: %s"
+                     (OpamFilename.Base.to_string f) (Printexc.to_string err))
+                patching_errors)
+         else "") ^
+        (if subst_errs <> [] then
+           Printf.sprintf "String expansion failed for these files:\n%s"
+             (OpamStd.Format.itemize
+                (fun (b,err) ->
+                   Printf.sprintf "%s.in: %s" (OpamFilename.Base.to_string b)
+                     (Printexc.to_string err))
+                subst_errs)
+         else "")
+      in
+      Some (Failure msg)
+    else
+      None
 
 let prepare_package_source st nv dir =
   log "prepare_package_source: %a at %a"
@@ -517,7 +511,7 @@ let prepare_package_source st nv dir =
   get_extra_sources_job @@+ function Some _ as err -> Done err | None ->
     check_extra_files |> function Some _ as err -> Done err | None ->
       let opam = OpamSwitchState.opam st nv in
-      prepare_package_build (OpamPackageVar.resolve ~opam st) opam nv dir
+      Done (prepare_package_build (OpamPackageVar.resolve ~opam st) opam nv dir)
 
 let compilation_env t opam =
   let build_env =
diff --git a/src/client/opamAction.mli b/src/client/opamAction.mli
index 029f1b203b4..419f0bc833a 100644
--- a/src/client/opamAction.mli
+++ b/src/client/opamAction.mli
@@ -40,7 +40,7 @@ val prepare_package_source:
     of `prepare_package_source`, without requiring a switch and
     without handling extra downloads. *)
 val prepare_package_build:
-  OpamFilter.env -> OpamFile.OPAM.t -> package -> dirname -> exn option OpamProcess.job
+  OpamFilter.env -> OpamFile.OPAM.t -> package -> dirname -> exn option
 
 (** [build_package t build_dir pkg] builds the package [pkg] within [build_dir].
     Returns [None] on success, [Some exn] on error.
diff --git a/src/client/opamInitDefaults.ml b/src/client/opamInitDefaults.ml
index c077b787766..e92711ad1db 100644
--- a/src/client/opamInitDefaults.ml
+++ b/src/client/opamInitDefaults.ml
@@ -52,11 +52,6 @@ let not_win32_filter =
   FOp (FIdent ([], OpamVariable.of_string "os", None), `Neq, FString "win32")
 let sandbox_filter = FOr (linux_filter, macos_filter)
 
-let gpatch_filter =
-  FOr (FOr (openbsd_filter, netbsd_filter),
-       FOr (freebsd_filter, FOr (dragonflybsd_filter, macos_filter)))
-let patch_filter = FNot gpatch_filter
-
 let gtar_filter = openbsd_filter
 let tar_filter = FNot gtar_filter
 
@@ -132,8 +127,6 @@ let required_tools ~sandboxing () =
   req_dl_tools () @
   [
     ["diff"], None, None;
-    ["patch"], None, Some patch_filter;
-    ["gpatch"], None, Some gpatch_filter;
     ["tar"], None, Some tar_filter;
     ["gtar"], None, Some gtar_filter;
     ["unzip"], None, None;
@@ -148,7 +141,6 @@ let required_packages_for_cygwin =
   [
     "diffutils";
     "make";
-    "patch";
     "tar";
     "unzip";
     "rsync";
diff --git a/src/core/dune b/src/core/dune
index 89beb7e47ea..df971773c48 100644
--- a/src/core/dune
+++ b/src/core/dune
@@ -3,7 +3,7 @@
   (public_name opam-core)
   (synopsis    "OCaml Package Manager core internal stdlib")
   ; TODO: Remove (re_export ...) when CI uses the OCaml version that includes https://github.com/ocaml/ocaml/pull/11989
-  (libraries   re (re_export ocamlgraph) unix sha jsonm swhid_core uutf)
+  (libraries   re (re_export ocamlgraph) unix sha jsonm swhid_core uutf patch)
   (flags       (:standard
                (:include ../ocaml-flags-standard.sexp)
                (:include ../ocaml-flags-configure.sexp)
diff --git a/src/core/opamFilename.ml b/src/core/opamFilename.ml
index 1806b9d3323..bd438f89cc8 100644
--- a/src/core/opamFilename.ml
+++ b/src/core/opamFilename.ml
@@ -445,8 +445,9 @@ let link ?(relative=false) ~target ~link =
   OpamSystem.link target (to_string link)
 [@@ocaml.warning "-16"]
 
-let patch ?preprocess filename dirname =
-  OpamSystem.patch ?preprocess ~dir:(Dir.to_string dirname) (to_string filename)
+let patch ?preprocess ~allow_unclean filename dirname =
+  OpamSystem.patch ?preprocess ~allow_unclean ~dir:(Dir.to_string dirname)
+    (to_string filename)
 
 let flock flag ?dontblock file = OpamSystem.flock flag ?dontblock (to_string file)
 
diff --git a/src/core/opamFilename.mli b/src/core/opamFilename.mli
index c9b2589ff4f..1b571223967 100644
--- a/src/core/opamFilename.mli
+++ b/src/core/opamFilename.mli
@@ -271,8 +271,12 @@ val remove_prefix_dir: Dir.t -> Dir.t -> string
 val remove_suffix: Base.t -> t -> string
 
 (** Apply a patch in a directory. If [preprocess] is set to false, there is no
-    CRLF translation. Returns [None] on success, the process error otherwise *)
-val patch: ?preprocess:bool -> t -> Dir.t -> exn option OpamProcess.job
+    CRLF translation. Returns [None] on success, the process error otherwise.
+
+    @param allow_unclean decides if applying a patch on a directory which
+    differs slightly from the one described in the patch file is allowed.
+    Allowing unclean applications imitates the default behaviour of GNU Patch. *)
+val patch: ?preprocess:bool -> allow_unclean:bool -> t -> Dir.t -> exn option
 
 (** Create an empty file *)
 val touch: t -> unit
diff --git a/src/core/opamSystem.ml b/src/core/opamSystem.ml
index deb8515142e..23779496133 100644
--- a/src/core/opamSystem.ml
+++ b/src/core/opamSystem.ml
@@ -1588,41 +1588,73 @@ let translate_patch ~dir orig corrected =
   end;
   close_in ch
 
-let gpatch = lazy begin
-  let rec search_gpatch = function
-    | [] -> None
-    | patch_cmd::patch_cmds ->
-      match OpamProcess.run (make_command ~name:"patch" patch_cmd ["--version"]) with
-      | r ->
-        (match OpamProcess.is_success r, r.OpamProcess.r_stdout with
-         | true, full::_ when
-             OpamStd.String.is_prefix_of ~from:0 ~full "GNU patch " ->
-           Some patch_cmd
-         | _ ->
-           search_gpatch patch_cmds)
-      | exception _ -> search_gpatch patch_cmds
+exception Internal_patch_error of string
+
+let internal_patch ~allow_unclean ~patch_filename ~dir diffs =
+  let internal_patch_error fmt =
+    Printf.ksprintf (fun str -> raise (Internal_patch_error str)) fmt
   in
-  let default_cmd, other_cmds =
-    match OpamStd.Sys.os () with
-    | Darwin
-    | DragonFly
-    | FreeBSD
-    | NetBSD
-    | OpenBSD -> ("gpatch", ["patch"])
-    | Cygwin
-    | Linux
-    | Unix
-    | Win32
-    | Other _ -> ("patch", ["gpatch"])
+  (* NOTE: It is important to keep this `concat dir ""` to ensure the
+     is_prefix_of below doesn't match another similarly named directory *)
+  let dir = Filename.concat (real_path dir) "" in
+  let get_path file =
+    let file = real_path (Filename.concat dir file) in
+    if not (OpamStd.String.is_prefix_of ~from:0 ~full:file dir) then
+      internal_patch_error "Patch %S tried to escape its scope."
+        patch_filename;
+    file
   in
-  match search_gpatch (default_cmd :: other_cmds) with
-  | Some gpatch -> gpatch
-  | None ->
-    OpamConsole.warning "Invalid patch utility. Please install GNU patch";
-    default_cmd
-end
+  let patch ~file content diff =
+    (* NOTE: The None case returned by [Patch.patch] is only returned
+       if [diff = Patch.Delete _]. This sub-function is not called in
+       this case so we [assert false] instead. *)
+    match Patch.patch ~cleanly:true content diff with
+    | Some x -> x
+    | None -> assert false (* See NOTE above *)
+    | exception _ when not allow_unclean ->
+      internal_patch_error "Patch %S does not apply cleanly."
+        patch_filename
+    | exception _ ->
+      match Patch.patch ~cleanly:false content diff with
+      | Some x ->
+        OpamStd.Option.iter (write (file^".orig")) content;
+        x
+      | None -> assert false (* See NOTE above *)
+      | exception _ ->
+        OpamStd.Option.iter (write (file^".orig")) content;
+        write (file^".rej") (Format.asprintf "%a" Patch.pp diff);
+        internal_patch_error "Patch %S does not apply cleanly."
+          patch_filename
+  in
+  let apply diff = match diff.Patch.operation with
+    | Patch.Edit (file1, file2) ->
+      (* That seems to be the GNU patch behaviour *)
+      let file =
+        let file1 = get_path file1 in
+        if Sys.file_exists file1 then
+          file1
+        else
+          get_path file2
+      in
+      let content = read file in
+      let content = patch ~file:file (Some content) diff in
+      write file content;
+    | Patch.Delete file ->
+      let file = get_path file in
+      remove_file_t ~with_log:false file
+    | Patch.Create file ->
+      let file = get_path file in
+      let content = patch ~file None diff in
+      write file content
+    | Patch.Rename_only (src, dst) ->
+      let src = get_path src in
+      let dst = get_path dst in
+      (* we use rename as we have all guarantee *)
+      Unix.rename src dst
+  in
+  List.iter apply diffs
 
-let patch ?(preprocess=true) ~dir p =
+let patch ?(preprocess=true) ~allow_unclean ~dir p =
   if not (Sys.file_exists p) then
     (OpamConsole.error "Patch file %S not found." p;
      raise Not_found);
@@ -1634,11 +1666,13 @@ let patch ?(preprocess=true) ~dir p =
     else
       p
   in
-  let patch_cmd = Lazy.force gpatch in
-  make_command ~name:"patch" ~dir patch_cmd ["-p1"; "-i"; p'] @@> fun r ->
+  let content = read p' in
+  try
+    let diffs = Patch.parse ~p:1 content in
+    internal_patch ~allow_unclean ~patch_filename:p ~dir diffs;
     if not (OpamConsole.debug ()) then Sys.remove p';
-    if OpamProcess.is_success r then Done None
-    else Done (Some (Process_error r))
+    None
+  with exn -> Some exn
 
 let register_printer () =
   Printexc.register_printer (function
diff --git a/src/core/opamSystem.mli b/src/core/opamSystem.mli
index 9f8e3de2a9d..52bff39b393 100644
--- a/src/core/opamSystem.mli
+++ b/src/core/opamSystem.mli
@@ -327,8 +327,12 @@ val get_lock_fd: lock -> Unix.file_descr
 
 (** Apply a patch file in the current directory. If [preprocess] is set to
     false, there is no CRLF translation. Returns the error if the patch didn't
-    apply. *)
-val patch: ?preprocess:bool -> dir:string -> string -> exn option OpamProcess.job
+    apply.
+
+    @param allow_unclean decides if applying a patch on a directory which
+    differs slightly from the one described in the patch file is allowed.
+    Allowing unclean applications imitates the default behaviour of GNU Patch. *)
+val patch: ?preprocess:bool -> allow_unclean:bool -> dir:string -> string -> exn option
 
 (** Returns the end-of-line encoding style for the given file. [None] means that
     either the encoding of line endings is mixed, or the file contains no line
diff --git a/src/repository/opamRepository.ml b/src/repository/opamRepository.ml
index 1ff3eddcca4..d18d9131041 100644
--- a/src/repository/opamRepository.ml
+++ b/src/repository/opamRepository.ml
@@ -538,11 +538,11 @@ let apply_repo_update repo repo_root = function
       | `http | `rsync -> false
       | _ -> true
     in
-    (OpamFilename.patch ~preprocess f repo_root @@+ function
-      | Some e ->
-        if not (OpamConsole.debug ()) then OpamFilename.remove f;
-        raise e
-      | None -> OpamFilename.remove f; Done ())
+    (match OpamFilename.patch ~preprocess ~allow_unclean:false f repo_root with
+     | Some e ->
+       if not (OpamConsole.debug ()) then OpamFilename.remove f;
+       raise e
+     | None -> OpamFilename.remove f; Done ())
   | Update_empty ->
     OpamConsole.msg "[%s] no changes from %s\n"
       (OpamConsole.colorise `green
diff --git a/src_ext/Makefile b/src_ext/Makefile
index 6df8f66cce9..30b5b446852 100644
--- a/src_ext/Makefile
+++ b/src_ext/Makefile
@@ -22,7 +22,10 @@ ifndef FETCH
   endif
 endif
 
-SRC_EXTS = cppo base64 extlib re cmdliner ocamlgraph cudf dose3 opam-file-format seq stdlib-shims spdx_licenses opam-0install-cudf 0install-solver uutf jsonm sha swhid_core menhir
+SRC_EXTS = \
+  cppo base64 extlib re cmdliner ocamlgraph cudf dose3 opam-file-format seq \
+  stdlib-shims spdx_licenses opam-0install-cudf 0install-solver uutf \
+  jsonm sha swhid_core menhir patch
 
 ifeq ($(MCCS_ENABLED),true)
 SRC_EXTS := $(SRC_EXTS) mccs
diff --git a/src_ext/Makefile.sources b/src_ext/Makefile.sources
index 01edf1a2989..6bf1bf8fc51 100644
--- a/src_ext/Makefile.sources
+++ b/src_ext/Makefile.sources
@@ -59,3 +59,6 @@ MD5_swhid_core = 77d88d4b1d96261c866f140c64d89af8
 
 URL_menhir = https://gitlab.inria.fr/fpottier/menhir/-/archive/20240715/archive.tar.gz
 MD5_menhir = d39a8943fe1be28199e5ec1f4133504c
+
+URL_patch = https://github.com/hannesm/patch/releases/download/v3.0.0-alpha1/patch-3.0.0-alpha1.tar.gz
+MD5_patch = 03aa87f8500c9caf4a73b2299c19b514
diff --git a/tests/reftests/repository.test b/tests/reftests/repository.test
index fa07335b318..af182d775e7 100644
--- a/tests/reftests/repository.test
+++ b/tests/reftests/repository.test
@@ -18,10 +18,8 @@ some content
 ### sh hash.sh REPO foo.1
 ### : Internal repository storage as archive or plain directory :
 ### opam switch create tarring --empty
-### opam update -vv | grep '^\+' | sed-cmd diff | sed-cmd patch | sed-cmd gpatch | '\+ gpatch ' -> '+ patch ' | 'patch-[^"]+' -> 'patch'
+### opam update -vv | grep '^\+' | sed-cmd diff
 + diff "-ruaN" "default" "default.new" (CWD=${BASEDIR}/OPAM/repo)
-+ patch "--version"
-+ patch "-p1" "-i" "${BASEDIR}/OPAM/log/patch" (CWD=${BASEDIR}/OPAM/repo/default)
 ### ls $OPAMROOT/repo | grep -v "cache"
 default
 lock
@@ -38,10 +36,8 @@ build: ["test" "-f" "baz"]
 ### <REPO/packages/foo/foo.2/files/baz>
 some content
 ### sh hash.sh REPO foo.2
-### opam update default -vv | grep '^\+' | sed-cmd tar | sed-cmd diff | sed-cmd patch | sed-cmd gpatch | '\+ gpatch ' -> '+ patch ' | 'patch-[^"]+' -> 'patch'
+### opam update default -vv | grep '^\+' | sed-cmd tar | sed-cmd diff
 + diff "-ruaN" "default" "default.new" (CWD=${BASEDIR}/OPAM/repo)
-+ patch "--version"
-+ patch "-p1" "-i" "${BASEDIR}/OPAM/log/patch" (CWD=${BASEDIR}/OPAM/repo/default)
 + tar "cfz" "${BASEDIR}/OPAM/repo/default.tar.gz.tmp" "-C" "${BASEDIR}/OPAM/repo" "default"
 ### ls $OPAMROOT/repo | grep -v "cache"
 default.tar.gz
@@ -78,11 +74,9 @@ build: ["test" "-f" "baz"]
 ### <REPO/packages/foo/foo.4/files/baz>
 some content
 ### sh hash.sh REPO foo.4
-### opam update -vv | grep '^\+' | sed-cmd tar | sed-cmd diff | sed-cmd patch | sed-cmd gpatch | '\+ gpatch ' -> '+ patch ' | 'patch-[^"]+' -> 'patch'
+### opam update -vv | grep '^\+' | sed-cmd tar | sed-cmd diff
 + tar "xfz" "${BASEDIR}/OPAM/repo/tarred.tar.gz" "-C" "${OPAMTMP}"
 + diff "-ruaN" "tarred" "tarred.new" (CWD=${OPAMTMP})
-+ patch "--version"
-+ patch "-p1" "-i" "${BASEDIR}/OPAM/log/patch" (CWD=${OPAMTMP}/tarred)
 + tar "cfz" "${BASEDIR}/OPAM/repo/tarred.tar.gz.tmp" "-C" "${OPAMTMP}" "tarred"
 ### opam install foo.4 -vv | grep '^\+' | sed-cmd test | sed-cmd tar
 + tar "xfz" "${BASEDIR}/OPAM/repo/tarred.tar.gz" "-C" "${OPAMTMP}"
@@ -102,11 +96,9 @@ build: ["test" "-f" "quux"]
 ### <REPO/packages/foo/foo.5/files/quux>
 some content
 ### sh hash.sh REPO foo.5
-### opam update -vv | grep '^\+' | sed-cmd tar | sed-cmd diff | sed-cmd patch | sed-cmd gpatch | '\+ gpatch ' -> '+ patch ' | 'patch-[^"]+' -> 'patch'
+### opam update -vv | grep '^\+' | sed-cmd tar | sed-cmd diff
 + tar "xfz" "${BASEDIR}/OPAM/repo/tarred.tar.gz" "-C" "${OPAMTMP}"
 + diff "-ruaN" "tarred" "tarred.new" (CWD=${OPAMTMP})
-+ patch "--version"
-+ patch "-p1" "-i" "${BASEDIR}/OPAM/log/patch" (CWD=${OPAMTMP}/tarred)
 ### opam install foo.5 -vv | grep '^\+' | sed-cmd test
 + test "-f" "quux" (CWD=${BASEDIR}/OPAM/tarring/.opam-switch/build/foo.5)
 ### ls $OPAMROOT/repo | grep -v "cache"

From 5a79d19e2a0d880d1d57bd9d8e65d360fdfe5efb Mon Sep 17 00:00:00 2001
From: Kate <kit-ty-kate@outlook.com>
Date: Wed, 26 Mar 2025 17:44:00 +0000
Subject: [PATCH 2/4] OpamSystem.patch: do not remove the original patch file
 if called with ~preprocess:false

---
 master_changes.md      | 1 +
 src/core/opamSystem.ml | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/master_changes.md b/master_changes.md
index 60a7c3388eb..9dae11f3897 100644
--- a/master_changes.md
+++ b/master_changes.md
@@ -275,5 +275,6 @@ users)
   * `OpamSystem.remove_dir`: do not fail with an exception when directory is a symbolic link [#6276 @btjorge @rjbou - fix #6275]
   * `OpamSystem.patch`: now returns `exn option` instead of `exn option OpamProcess.job` and no longer calls the system GNU Patch [#5892 @kit-ty-kate]
   * `OpamSystem.patch`: a named-parameter `~allow_unclean` was added [#5892 @kit-ty-kate]
+  * `OpamSystem.patch`: do not remove the original patch file if called with `~preprocess:false` [#5892 @kit-ty-kate]
   * `OpamParallel.*.{map,reduce,iter}`: Run `Gc.compact` when the main process is waiting for the children processes for the first time [#5396 @kkeundotnet]
   * `OpamSystem`, `OpamFilename`: add `with_tmp_file` and `with_tmp_file_job` function, that create a file name in temporary directory and removes it at the end of the call [#6036 @rjbou]
diff --git a/src/core/opamSystem.ml b/src/core/opamSystem.ml
index 23779496133..dfc4cf497dd 100644
--- a/src/core/opamSystem.ml
+++ b/src/core/opamSystem.ml
@@ -1670,7 +1670,7 @@ let patch ?(preprocess=true) ~allow_unclean ~dir p =
   try
     let diffs = Patch.parse ~p:1 content in
     internal_patch ~allow_unclean ~patch_filename:p ~dir diffs;
-    if not (OpamConsole.debug ()) then Sys.remove p';
+    if preprocess && not (OpamConsole.debug ()) then Sys.remove p';
     None
   with exn -> Some exn
 

From 4efcfb59a898df2c67cb32d37ff75ec89028eb28 Mon Sep 17 00:00:00 2001
From: Kate <kit-ty-kate@outlook.com>
Date: Wed, 26 Mar 2025 16:31:47 +0000
Subject: [PATCH 3/4] Replace the use of the system diff utility by the OCaml
 patch library

---
 master_changes.md                        |   8 +-
 src/client/opamInitDefaults.ml           |   2 -
 src/core/opamSystem.mli                  |   4 +
 src/repository/dune                      |   2 +-
 src/repository/opamHTTP.ml               |  17 ++-
 src/repository/opamLocal.ml              |   9 +-
 src/repository/opamRepositoryBackend.ml  | 127 +++++++++++++++++++----
 src/repository/opamRepositoryBackend.mli |  11 +-
 tests/reftests/repository.test           |  12 +--
 tests/reftests/update.test               |   1 -
 10 files changed, 140 insertions(+), 53 deletions(-)

diff --git a/master_changes.md b/master_changes.md
index 9dae11f3897..ea723d852c4 100644
--- a/master_changes.md
+++ b/master_changes.md
@@ -68,7 +68,7 @@ users)
   * [BUG] Do not show the not-up-to-date message with packages tagged with avoid-version [#6273 @kit-ty-kate - fix #6271]
   * [BUG] Fix a regression on `opam upgrade <package>` upgrading unrelated packages [#6373 @AltGr]
   * [BUG] Fix a regression on `opam upgrade --all <uninstalled-pkg>` not upgrading the whole switch [#6373 @kit-ty-kate]
-  * Updates are now applied using the `patch` OCaml library instead of the system GNU Patch [#5892 @kit-ty-kate - fix ocaml/setup-ocaml#933 #6052]
+  * Updates are now applied using the `patch` OCaml library instead of the system GNU Patch and diff utilities [#5892 @kit-ty-kate - fix ocaml/setup-ocaml#933 #6052]
 
 ## Tree
 
@@ -87,6 +87,7 @@ users)
   * Update SWH API request [#6036 @rjbou]
   * Rework SWH fallback to have a more correct archive retrieval and more fine grained error handling [#6036 @rjbou - fix #5721]
   * Check that the repositories given to `opam repository remove` actually exist [#5014 @kit-ty-kate - fixes #5012]
+  * ✘ Symlinks in repositories are no longer supported [#5892 @kit-ty-kate]
 
 ## Lock
   * [BUG] Fix `pin-depends` for `with-*` dependencies [#5471 @rjbou - fix #5428]
@@ -104,7 +105,7 @@ users)
   * Lookup at `gpatch` before `patch` on macOS now that both homebrew and macports expose `gpatch` as `gpatch` since Homebrew/homebrew-core#174687 [#6255 @kit-ty-kate]
   * Relax lookup on OpenBSD to consider all installed packages [#6362 @semarie]
   * Speedup the detection of available system packages with pacman and brew [#6324 @kit-ty-kate]
-  * The system GNU Patch is no longer runtime dependency of opam [#5892 @kit-ty-kate - fix #6052]
+  * The system GNU Patch and diff are no longer runtime dependencies of opam [#5892 @kit-ty-kate - fix #6052]
 
 ## Format upgrade
 
@@ -245,6 +246,8 @@ users)
   * `OpamDownload.download`: more fine grained HTTP request error code detection for curl [#6036 @rjbou]
   * `OpamRepository.revision`: now returns a `string` instead of a `version` [#6409 @kit-ty-kate]
   * `OpamRepositoryBackend.S.revision`: now returns a `string` instead of a `version` [#6409 @kit-ty-kate]
+  * `OpamRepositoryBackend.get_diff`: now returns `exn option` instead of `exn option OpamProcess.job` and no longer calls the system `diff` utility [#5892 @kit-ty-kate]
+  * `OpamRepositoryBackend.get_diff`: now raises `Stdlib.Failure` if an unsupported file type or comparison is detected [#5892 @kit-ty-kate]
 
 ## opam-state
   * `OpamStateConfig`: Make the `?lock_kind` parameters non-optional to avoid breaking the library users after they upgrade their opam root [#5488 @kit-ty-kate]
@@ -272,6 +275,7 @@ users)
   * `OpamStd.Sys.get_freebsd_version`: was added, which returns the output of the `uname -U` command [#6217 @kit-ty-kate]
   * `OpamStubs.get_stdout_ws_col`: new Unix-only function returning the number of columns of the current terminal window [#6244 @kit-ty-kate]
   * `OpamSystem`: add `is_archive_from_string` that does the same than `is_archive` but without looking at the file, only analysing the string (extension) [#6219 @rjbou]
+  * `OpamSystem.get_files`: was exposed which returns the list of files (without prefix) inside the given directory [#5892 @kit-ty-kate]
   * `OpamSystem.remove_dir`: do not fail with an exception when directory is a symbolic link [#6276 @btjorge @rjbou - fix #6275]
   * `OpamSystem.patch`: now returns `exn option` instead of `exn option OpamProcess.job` and no longer calls the system GNU Patch [#5892 @kit-ty-kate]
   * `OpamSystem.patch`: a named-parameter `~allow_unclean` was added [#5892 @kit-ty-kate]
diff --git a/src/client/opamInitDefaults.ml b/src/client/opamInitDefaults.ml
index e92711ad1db..5e6456023c5 100644
--- a/src/client/opamInitDefaults.ml
+++ b/src/client/opamInitDefaults.ml
@@ -126,7 +126,6 @@ let recommended_tools () =
 let required_tools ~sandboxing () =
   req_dl_tools () @
   [
-    ["diff"], None, None;
     ["tar"], None, Some tar_filter;
     ["gtar"], None, Some gtar_filter;
     ["unzip"], None, None;
@@ -139,7 +138,6 @@ let required_tools ~sandboxing () =
 
 let required_packages_for_cygwin =
   [
-    "diffutils";
     "make";
     "tar";
     "unzip";
diff --git a/src/core/opamSystem.mli b/src/core/opamSystem.mli
index 52bff39b393..4150ce13fda 100644
--- a/src/core/opamSystem.mli
+++ b/src/core/opamSystem.mli
@@ -125,6 +125,10 @@ val read: string -> string
     advisory write lock to prevent concurrent reads or writes) *)
 val write: string -> string -> unit
 
+(** [get_files dir] returns the list of files (without prefix) inside the
+    directory [dir]. *)
+val get_files : string -> string list
+
 (** [remove filename] removes [filename]. Works whether [filename] is
     a file or a directory *)
 val remove: string -> unit
diff --git a/src/repository/dune b/src/repository/dune
index cb622b218b4..0815ce885ea 100644
--- a/src/repository/dune
+++ b/src/repository/dune
@@ -3,7 +3,7 @@
   (public_name opam-repository)
   (synopsis    "OCaml Package Manager remote repository handling library")
   ; TODO: Remove (re_export ...) when CI uses the OCaml version that includes https://github.com/ocaml/ocaml/pull/11989
-  (libraries   (re_export opam-format))
+  (libraries   (re_export opam-format) patch)
   (flags       (:standard
                (:include ../ocaml-flags-standard.sexp)
                (:include ../ocaml-flags-configure.sexp)
diff --git a/src/repository/opamHTTP.ml b/src/repository/opamHTTP.ml
index 9c62d0ea231..fd4c4ac44e3 100644
--- a/src/repository/opamHTTP.ml
+++ b/src/repository/opamHTTP.ml
@@ -56,15 +56,14 @@ module B = struct
        OpamFilename.dir_is_empty repo_root then
       Done (OpamRepositoryBackend.Update_full quarantine)
     else
-      OpamProcess.Job.finally finalise @@ fun () ->
-      OpamRepositoryBackend.job_text repo_name "diff"
-        (OpamRepositoryBackend.get_diff
-           (OpamFilename.dirname_dir repo_root)
-           (OpamFilename.basename_dir repo_root)
-           (OpamFilename.basename_dir quarantine))
-      @@| function
-      | None -> OpamRepositoryBackend.Update_empty
-      | Some patch -> OpamRepositoryBackend.Update_patch patch
+      OpamStd.Exn.finally finalise @@ fun () ->
+      OpamRepositoryBackend.get_diff
+        (OpamFilename.dirname_dir repo_root)
+        (OpamFilename.basename_dir repo_root)
+        (OpamFilename.basename_dir quarantine)
+      |> function
+      | None -> Done OpamRepositoryBackend.Update_empty
+      | Some patch -> Done (OpamRepositoryBackend.Update_patch patch)
 
   let repo_update_complete _ _ = Done ()
 
diff --git a/src/repository/opamLocal.ml b/src/repository/opamLocal.ml
index 4b1f77d97da..5b08ed1be33 100644
--- a/src/repository/opamLocal.ml
+++ b/src/repository/opamLocal.ml
@@ -178,15 +178,14 @@ module B = struct
          OpamFilename.dir_is_empty repo_root then
         Done (OpamRepositoryBackend.Update_full quarantine)
       else
-        OpamProcess.Job.finally finalise @@ fun () ->
-        OpamRepositoryBackend.job_text repo_name "diff" @@
+        OpamStd.Exn.finally finalise @@ fun () ->
         OpamRepositoryBackend.get_diff
           (OpamFilename.dirname_dir repo_root)
           (OpamFilename.basename_dir repo_root)
           (OpamFilename.basename_dir quarantine)
-        @@| function
-        | None -> OpamRepositoryBackend.Update_empty
-        | Some p -> OpamRepositoryBackend.Update_patch p
+        |> function
+        | None -> Done OpamRepositoryBackend.Update_empty
+        | Some p -> Done (OpamRepositoryBackend.Update_patch p)
 
   let repo_update_complete _ _ = Done ()
 
diff --git a/src/repository/opamRepositoryBackend.ml b/src/repository/opamRepositoryBackend.ml
index fbc9305f2a1..ec3e4d8461b 100644
--- a/src/repository/opamRepositoryBackend.ml
+++ b/src/repository/opamRepositoryBackend.ml
@@ -10,7 +10,7 @@
 
 open OpamTypes
 
-let log = OpamConsole.log "REPO_BACKEND"
+let log ?level fmt = OpamConsole.log "REPO_BACKEND" ?level fmt
 let slog = OpamConsole.slog
 
 type update =
@@ -65,33 +65,120 @@ let check_digest filename = function
        false)
   | _ -> true
 
-open OpamProcess.Job.Op
-
 let job_text name label =
   OpamProcess.Job.with_text
     (Printf.sprintf "[%s: %s]"
        (OpamConsole.colorise `green (OpamRepositoryName.to_string name))
        label)
 
+let get_files_for_diff parent_dir dir1 dir2 =
+  let getfiles parent_dir dir =
+    let dir = Filename.concat (OpamFilename.Dir.to_string parent_dir) dir in
+    OpamSystem.get_files dir
+  in
+  match dir1, dir2 with
+  | None, None -> assert false
+  | Some dir, None ->
+    List.map (fun file -> Patch.Delete (dir^"/"^file))
+      (getfiles parent_dir dir)
+  | None, Some dir ->
+    List.map (fun file -> Patch.Create (dir^"/"^file))
+      (getfiles parent_dir dir)
+  | Some dir1, Some dir2 ->
+    let files1 = List.fast_sort String.compare (getfiles parent_dir dir1) in
+    let files2 = List.fast_sort String.compare (getfiles parent_dir dir2) in
+    let rec aux acc files1 files2 = match files1, files2 with
+      | (file1::files1 as orig1), (file2::files2 as orig2) ->
+        let cmp = String.compare file1 file2 in
+        if cmp = 0 then
+          aux (Patch.Edit
+                 (dir1^"/"^file1, dir2^"/"^file2)
+               :: acc)
+            files1 files2
+        else if cmp < 0 then
+          aux (Patch.Delete (dir1^"/"^file1) :: acc) files1 orig2
+        else
+          aux (Patch.Create (dir2^"/"^file2) :: acc) orig1 files2
+      | file1::files1, [] ->
+        aux (Patch.Delete (dir1^"/"^file1) :: acc) files1 []
+      | [], file2::files2 ->
+        aux (Patch.Create (dir2^"/"^file2) :: acc) [] files2
+      | [], [] ->
+        acc
+    in
+    aux [] files1 files2
+
 let get_diff parent_dir dir1 dir2 =
+  let chrono = OpamConsole.timer () in
   log "diff: %a/{%a,%a}"
     (slog OpamFilename.Dir.to_string) parent_dir
     (slog OpamFilename.Base.to_string) dir1
     (slog OpamFilename.Base.to_string) dir2;
-  let patch = OpamSystem.temp_file ~auto_clean: false "patch" in
-  let patch_file = OpamFilename.of_string patch in
-  let finalise () = OpamFilename.remove patch_file in
-  OpamProcess.Job.catch (fun e -> finalise (); raise e) @@ fun () ->
-  OpamSystem.make_command
-    ~verbose:OpamCoreConfig.(!r.verbose_level >= 2)
-    ~dir:(OpamFilename.Dir.to_string parent_dir) ~stdout:patch
-    "diff"
-    [ "-ruaN";
-      OpamFilename.Base.to_string dir1;
-      OpamFilename.Base.to_string dir2; ]
-  @@> function
-  | { OpamProcess.r_code = 0; _ } -> finalise(); Done None
-  | { OpamProcess.r_code = 1; _ } as r ->
-    OpamProcess.cleanup ~force:true r;
-    Done (Some patch_file)
-  | r -> OpamSystem.process_error r
+  let readfile parent_dir file =
+    let file = Filename.concat (OpamFilename.Dir.to_string parent_dir) file in
+    OpamSystem.read file
+  in
+  let lstat_opt parent_dir = function
+    | None -> None
+    | Some file ->
+      let file = Filename.concat (OpamFilename.Dir.to_string parent_dir) file in
+      Some (Unix.lstat file)
+  in
+  let rec aux diffs dir1 dir2 =
+    let files = get_files_for_diff parent_dir dir1 dir2 in
+    let diffs =
+      List.fold_left (fun diffs operation ->
+          let file1, file2 = match operation with
+            | Patch.Delete filename -> (Some filename, None)
+            | Patch.Create filename -> (None, Some filename)
+            | Patch.Edit (file1, file2)
+            | Patch.Rename_only (file1, file2) -> (Some file1, Some file2)
+          in
+          let add_to_diffs content1 content2 diffs =
+            match Patch.diff operation content1 content2 with
+            | None -> diffs
+            | Some diff -> diff :: diffs
+          in
+          match lstat_opt parent_dir file1, lstat_opt parent_dir file2 with
+          | Some {st_kind = S_REG; _}, None
+          | None, Some {st_kind = S_REG; _}
+          | Some {st_kind = S_REG; _}, Some {st_kind = S_REG; _} ->
+            let content1 = Option.map (readfile parent_dir) file1 in
+            let content2 = Option.map (readfile parent_dir) file2 in
+            add_to_diffs content1 content2 diffs
+          | Some {st_kind = S_DIR; _}, None | None, Some {st_kind = S_DIR; _}
+          | Some {st_kind = S_DIR; _}, Some {st_kind = S_DIR; _} ->
+            aux diffs file1 file2
+          | Some {st_kind = S_DIR; _}, Some {st_kind = S_REG; _} ->
+            failwith "Change from a directory to a regular file is unsupported"
+          | Some {st_kind = S_REG; _}, Some {st_kind = S_DIR; _} ->
+            failwith "Change from a regular file to a directory is unsupported"
+          | Some {st_kind = S_LNK; _}, _ | _, Some {st_kind = S_LNK; _} ->
+            failwith "Symlinks are unsupported"
+          | Some {st_kind = S_CHR; _}, _ | _, Some {st_kind = S_CHR; _} ->
+            failwith "Character devices are unsupported"
+          | Some {st_kind = S_BLK; _}, _ | _, Some {st_kind = S_BLK; _} ->
+            failwith "Block devices are unsupported"
+          | Some {st_kind = S_FIFO; _}, _ | _, Some {st_kind = S_FIFO; _} ->
+            failwith "Named pipes are unsupported"
+          | Some {st_kind = S_SOCK; _}, _ | _, Some {st_kind = S_SOCK; _} ->
+            failwith "Sockets are unsupported"
+          | None, None -> assert false)
+        diffs files
+    in
+    diffs
+  in
+  match
+    aux []
+      (Some (OpamFilename.Base.to_string dir1))
+      (Some (OpamFilename.Base.to_string dir2))
+  with
+  | [] ->
+    log "Internal diff (empty) done in %.2fs." (chrono ());
+    None
+  | diffs ->
+    log "Internal diff (non-empty) done in %.2fs." (chrono ());
+    let patch = OpamSystem.temp_file ~auto_clean:false "patch" in
+    let patch_file = OpamFilename.of_string patch in
+    OpamFilename.write patch_file (Format.asprintf "%a" Patch.pp_list diffs);
+    Some patch_file
diff --git a/src/repository/opamRepositoryBackend.mli b/src/repository/opamRepositoryBackend.mli
index 1c03b885413..107911b794f 100644
--- a/src/repository/opamRepositoryBackend.mli
+++ b/src/repository/opamRepositoryBackend.mli
@@ -111,8 +111,9 @@ val job_text:
     subdirs of [parent_dir], returns None if they are equal, and the
     corresponding patch otherwise.
 
-    Note: this relies on the [diff -ruN] command, a built-in diff may be more
-    portable -- in particular, [-u], [-N] are not POSIX, and recursive diffs
-    might not be completely reliable. It also assumes text files only, and fails
-    otherwise. *)
-val get_diff: dirname -> basename -> basename -> filename option OpamProcess.job
+    @raise Stdlib.Failure if an unsupported file type or comparison is
+    detected in any of [subdir1] or [subdir2].
+    Unsupported file types: symlinks, character devices, block devices,
+    named pipes, sockets.
+    Unsupported comparison: comparison between regular files and directories. *)
+val get_diff: dirname -> basename -> basename -> filename option
diff --git a/tests/reftests/repository.test b/tests/reftests/repository.test
index af182d775e7..cbc0890dba0 100644
--- a/tests/reftests/repository.test
+++ b/tests/reftests/repository.test
@@ -18,8 +18,7 @@ some content
 ### sh hash.sh REPO foo.1
 ### : Internal repository storage as archive or plain directory :
 ### opam switch create tarring --empty
-### opam update -vv | grep '^\+' | sed-cmd diff
-+ diff "-ruaN" "default" "default.new" (CWD=${BASEDIR}/OPAM/repo)
+### opam update -vv | grep '^\+'
 ### ls $OPAMROOT/repo | grep -v "cache"
 default
 lock
@@ -36,8 +35,7 @@ build: ["test" "-f" "baz"]
 ### <REPO/packages/foo/foo.2/files/baz>
 some content
 ### sh hash.sh REPO foo.2
-### opam update default -vv | grep '^\+' | sed-cmd tar | sed-cmd diff
-+ diff "-ruaN" "default" "default.new" (CWD=${BASEDIR}/OPAM/repo)
+### opam update default -vv | grep '^\+' | sed-cmd tar
 + tar "cfz" "${BASEDIR}/OPAM/repo/default.tar.gz.tmp" "-C" "${BASEDIR}/OPAM/repo" "default"
 ### ls $OPAMROOT/repo | grep -v "cache"
 default.tar.gz
@@ -74,9 +72,8 @@ build: ["test" "-f" "baz"]
 ### <REPO/packages/foo/foo.4/files/baz>
 some content
 ### sh hash.sh REPO foo.4
-### opam update -vv | grep '^\+' | sed-cmd tar | sed-cmd diff
+### opam update -vv | grep '^\+' | sed-cmd tar
 + tar "xfz" "${BASEDIR}/OPAM/repo/tarred.tar.gz" "-C" "${OPAMTMP}"
-+ diff "-ruaN" "tarred" "tarred.new" (CWD=${OPAMTMP})
 + tar "cfz" "${BASEDIR}/OPAM/repo/tarred.tar.gz.tmp" "-C" "${OPAMTMP}" "tarred"
 ### opam install foo.4 -vv | grep '^\+' | sed-cmd test | sed-cmd tar
 + tar "xfz" "${BASEDIR}/OPAM/repo/tarred.tar.gz" "-C" "${OPAMTMP}"
@@ -96,9 +93,8 @@ build: ["test" "-f" "quux"]
 ### <REPO/packages/foo/foo.5/files/quux>
 some content
 ### sh hash.sh REPO foo.5
-### opam update -vv | grep '^\+' | sed-cmd tar | sed-cmd diff
+### opam update -vv | grep '^\+' | sed-cmd tar
 + tar "xfz" "${BASEDIR}/OPAM/repo/tarred.tar.gz" "-C" "${OPAMTMP}"
-+ diff "-ruaN" "tarred" "tarred.new" (CWD=${OPAMTMP})
 ### opam install foo.5 -vv | grep '^\+' | sed-cmd test
 + test "-f" "quux" (CWD=${BASEDIR}/OPAM/tarring/.opam-switch/build/foo.5)
 ### ls $OPAMROOT/repo | grep -v "cache"
diff --git a/tests/reftests/update.test b/tests/reftests/update.test
index 568829b1c1c..69c62178226 100644
--- a/tests/reftests/update.test
+++ b/tests/reftests/update.test
@@ -4,7 +4,6 @@ opam-version: "2.0"
 ### opam update --verbose
 
 <><> Updating package repositories ><><><><><><><><><><><><><><><><><><><><><><>
-Processing  1/1: [default: rsync]
 [default] synchronised from file://${BASEDIR}/REPO
 Processing: [default: loading data]
 Now run 'opam upgrade' to apply any package updates.

From 9ad9ef5801cf0994c351e10c180485b91da7a619 Mon Sep 17 00:00:00 2001
From: Raja Boujbel <raja.boujbel@ocamlpro.com>
Date: Thu, 20 Mar 2025 15:42:40 +0100
Subject: [PATCH 4/4] Add a library test for the new OCaml implementation of
 patch and diff

---
 master_changes.md            |   1 +
 tests/lib/dune               |   5 +
 tests/lib/patchDiff.expected | 339 +++++++++++++++++++++++++++++++++++
 tests/lib/patchDiff.ml       | 312 ++++++++++++++++++++++++++++++++
 4 files changed, 657 insertions(+)
 create mode 100644 tests/lib/patchDiff.expected
 create mode 100644 tests/lib/patchDiff.ml

diff --git a/master_changes.md b/master_changes.md
index ea723d852c4..86d35dc6e5f 100644
--- a/master_changes.md
+++ b/master_changes.md
@@ -174,6 +174,7 @@ users)
 ## Internal: Windows
 
 ## Test
+  * Add a library test for the new OCaml implementation of patch and diff [#5892 @rjbou]
 
 ## Benchmarks
   * Add benchmarks for `opam show` [#6212 @kit-ty-kate]
diff --git a/tests/lib/dune b/tests/lib/dune
index 311c379869e..56108d82818 100644
--- a/tests/lib/dune
+++ b/tests/lib/dune
@@ -8,3 +8,8 @@
   (libraries opam-format)
   (modules TypeGymnastics)
   (action (run %{test})))
+
+(test
+  (name patchDiff)
+  (modules patchDiff)
+  (libraries opam-repository))
diff --git a/tests/lib/patchDiff.expected b/tests/lib/patchDiff.expected
new file mode 100644
index 00000000000..f24f4355d3a
--- /dev/null
+++ b/tests/lib/patchDiff.expected
@@ -0,0 +1,339 @@
+
+----------------------
+ Test 1: normal
+----------------------
+
+*** SETUP ***
++ first/
++ first/diff-dir-plus-fst
++ first/diff-dir-plus-fst/fst
+  > foo
++ first/diff-dir-plus-snd
++ first/diff-dir-plus-snd/fst
+  > foo
+  > bar
++ first/diff-file
+  > foo
++ first/diff-file-plus-fst
+  > foo
+  > bar
++ first/diff-file-plus-snd
+  > foo
++ first/dir-only-fst
++ first/dir-only-fst/fst
+  > foo
++ first/file-only-fst
+  > foo
++ first/same-file
+  > foo
++ second/
++ second/diff-dir-plus-fst
++ second/diff-dir-plus-fst/fst
+  > foo
+  > bar
++ second/diff-dir-plus-snd
++ second/diff-dir-plus-snd/fst
+  > foo
++ second/diff-file
+  > bar
++ second/diff-file-plus-fst
+  > foo
++ second/diff-file-plus-snd
+  > foo
+  > bar
++ second/file-only-snd
+  > foo
++ second/same-file
+  > foo
+
+*** DIFF ***
+--- first/diff-dir-plus-fst/fst
++++ second/diff-dir-plus-fst/fst
+@@ -2,0 +2,1 @@
++bar
+--- first/diff-dir-plus-snd/fst
++++ second/diff-dir-plus-snd/fst
+@@ -2,1 +2,0 @@
+-bar
+--- first/diff-file
++++ second/diff-file
+@@ -1,1 +1,1 @@
+-foo
++bar
+--- first/diff-file-plus-fst
++++ second/diff-file-plus-fst
+@@ -2,1 +2,0 @@
+-bar
+--- first/diff-file-plus-snd
++++ second/diff-file-plus-snd
+@@ -2,0 +2,1 @@
++bar
+--- first/dir-only-fst/fst
++++ /dev/null
+@@ -1,1 +0,0 @@
+-foo
+--- first/file-only-fst
++++ /dev/null
+@@ -1,1 +0,0 @@
+-foo
+--- /dev/null
++++ second/file-only-snd
+@@ -0,0 +1,1 @@
++foo
+
+*** PATCHED ***
++ first/
++ first/diff-dir-plus-fst
++ first/diff-dir-plus-fst/fst
+  > foo
+  > bar
++ first/diff-dir-plus-snd
++ first/diff-dir-plus-snd/fst
+  > foo
++ first/diff-file
+  > bar
++ first/diff-file-plus-fst
+  > foo
++ first/diff-file-plus-snd
+  > foo
+  > bar
++ first/dir-only-fst
++ first/file-only-snd
+  > foo
++ first/same-file
+  > foo
++ second/
++ second/diff-dir-plus-fst
++ second/diff-dir-plus-fst/fst
+  > foo
+  > bar
++ second/diff-dir-plus-snd
++ second/diff-dir-plus-snd/fst
+  > foo
++ second/diff-file
+  > bar
++ second/diff-file-plus-fst
+  > foo
++ second/diff-file-plus-snd
+  > foo
+  > bar
++ second/file-only-snd
+  > foo
++ second/same-file
+  > foo
+
+
+----------------------
+ Test 2: diff file/dir error
+----------------------
+
+*** SETUP ***
++ first/
++ first/file-fst-dir-snd
+  > foo
++ first/same-file
+  > foo
++ second/
++ second/file-fst-dir-snd
++ second/file-fst-dir-snd/fst
+  > foo
++ second/same-file
+  > foo
+
+*** DIFF ***
+ERROR: Change from a regular file to a directory is unsupported
+
+----------------------
+ Test 3: diff dir/file error
+----------------------
+
+*** SETUP ***
++ first/
++ first/dir-fst-file-snd
++ first/dir-fst-file-snd/fst
+  > foo
++ first/same-file
+  > foo
++ second/
++ second/dir-fst-file-snd
+  > foo
++ second/same-file
+  > foo
+
+*** DIFF ***
+ERROR: Change from a directory to a regular file is unsupported
+
+----------------------
+ Test 4: symlink fst
+----------------------
+
+*** SETUP ***
++ first/
++ first/linked-file-fst
+  > bar
++ first/same-file
+  > foo
++ second/
++ second/linked-file-fst
+  > foo
++ second/same-file
+  > foo
+
+*** DIFF ***
+ERROR: Symlinks are unsupported
+
+----------------------
+ Test 5: symlink snd
+----------------------
+
+*** SETUP ***
++ first/
++ first/linked-file-snd
+  > foo
++ first/same-file
+  > foo
++ second/
++ second/linked-file-snd
+  > bar
++ second/same-file
+  > foo
+
+*** DIFF ***
+ERROR: Symlinks are unsupported
+
+----------------------
+ Test 6: hardlink fst
+----------------------
+
+*** SETUP ***
++ first/
++ first/hardlinked-file-fst
+  > bar
++ first/same-file
+  > foo
++ second/
++ second/hardlinked-file-fst
+  > foo
++ second/same-file
+  > foo
+
+*** DIFF ***
+--- first/hardlinked-file-fst
++++ second/hardlinked-file-fst
+@@ -1,1 +1,1 @@
+-bar
++foo
+
+*** PATCHED ***
++ first/
++ first/hardlinked-file-fst
+  > foo
++ first/same-file
+  > foo
++ second/
++ second/hardlinked-file-fst
+  > foo
++ second/same-file
+  > foo
+
+
+----------------------
+ Test 7: hardlink snd
+----------------------
+
+*** SETUP ***
++ first/
++ first/hardlinked-file-snd
+  > foo
++ first/same-file
+  > foo
++ second/
++ second/hardlinked-file-snd
+  > foo
++ second/same-file
+  > foo
+
+*** DIFF ***
+No diff
+
+----------------------
+ Test 8: patch error garbage
+----------------------
+
+*** SETUP ***
++ first/
++ first/diff-file
+  > foo
++ first/same-file
+  > foo
++ second/
++ second/diff-file
+  > bar
++ second/same-file
+  > foo
+
+*** GIVEN DIFF ***
+something in
+the file
+that is not
+patch format
+
+*** PATCHED ***
++ first/
++ first/diff-file
+  > foo
++ first/same-file
+  > foo
++ second/
++ second/diff-file
+  > bar
++ second/same-file
+  > foo
+
+
+----------------------
+ Test 9: patch truncated
+----------------------
+
+*** SETUP ***
++ first/
++ first/diff-file
+  > foo
++ first/diff-file-plus-fst
+  > foo
+  > bar
++ first/same-file
+  > foo
++ second/
++ second/diff-file
+  > bar
++ second/diff-file-plus-fst
+  > foo
++ second/same-file
+  > foo
+
+*** GIVEN DIFF ***
+--- first/diff-file
++++ second/diff-file
+@@ -1,1 +1,1 @@
+-foo
++bar
+--- first/diff-fi
+
+*** PATCHED ***
++ first/
++ first/diff-file
+  > bar
++ first/diff-file-plus-fst
+  > foo
+  > bar
++ first/same-file
+  > foo
++ second/
++ second/diff-file
+  > bar
++ second/diff-file-plus-fst
+  > foo
++ second/same-file
+  > foo
+
diff --git a/tests/lib/patchDiff.ml b/tests/lib/patchDiff.ml
new file mode 100644
index 00000000000..28fccb7d9d1
--- /dev/null
+++ b/tests/lib/patchDiff.ml
@@ -0,0 +1,312 @@
+type content =
+  | File of string (* file *)
+  | Dir of (string * string) list (* directory with list filename * content *)
+  | Symlink (* Soft Link *)
+  | Hardlink (* Hard link *)
+  | V (* void *)
+
+type arborescence = {
+  name: string;
+  first : content;
+  second : content;
+}
+
+(** Contents *)
+
+let foo = "foo\n"
+let bar = "bar\n"
+let foobar = "foo\nbar\n"
+let same_file = {
+  name = "same-file";
+  first = File foo;
+  second = File foo;
+}
+let diff_file = {
+  name = "diff-file";
+  first = File foo;
+  second = File bar;
+}
+let diff_file_plus_fst = {
+  name = "diff-file-plus-fst";
+  first = File foobar;
+  second = File foo;
+}
+let diff_file_plus_snd = {
+  name = "diff-file-plus-snd";
+  first = File foo;
+  second = File foobar;
+}
+
+let content_working_diff = [
+  same_file;
+  diff_file;
+  diff_file_plus_fst;
+  diff_file_plus_snd;
+  { name = "diff-file";
+    first = File foo;
+    second = File bar;
+  };
+  { name = "diff-file-plus-fst";
+    first = File foobar;
+    second = File foo;
+  };
+  { name = "diff-file-plus-snd";
+    first = File foo;
+    second = File foobar;
+  };
+  { name = "file-only-fst";
+    first = File foo;
+    second = V;
+  };
+  { name = "file-only-snd";
+    first = V;
+    second = File foo;
+  };
+  { name = "same-dir";
+    first = Dir [];
+    second = Dir [];
+  };
+  { name = "diff-dir-plus-fst";
+    first = Dir [ "fst", foo ];
+    second = Dir [ "fst", foobar ] ;
+  };
+  { name = "diff-dir-plus-snd";
+    first = Dir [ "fst", foobar ];
+    second = Dir [ "fst", foo ];
+  };
+  { name = "dir-only-fst";
+    first = Dir [ "fst", foo ];
+    second = V;
+  };
+]
+
+let content_dir_file = [
+  same_file;
+  { name = "file-fst-dir-snd";
+    first = File foo;
+    second = Dir [ "fst", foo];
+  };
+]
+
+let content_file_dir = [
+  same_file;
+  { name = "dir-fst-file-snd";
+    first = Dir [ "fst", foo ];
+    second = File foo;
+  };
+]
+
+let content_symlink_fst = [
+  same_file;
+  { name = "linked-file-fst";
+    first = Symlink;
+    second = File foo;
+  };
+]
+
+let content_symlink_snd = [
+  same_file;
+  { name = "linked-file-snd";
+    first = File foo;
+    second = Symlink;
+  };
+]
+
+let content_hardlink_fst = [
+  same_file;
+  { name = "hardlinked-file-fst";
+    first = Hardlink;
+    second = File foo;
+  };
+]
+
+let content_hardlink_snd = [
+  same_file;
+  { name = "hardlinked-file-snd";
+    first = File foo;
+    second = Hardlink;
+  };
+]
+
+
+let content_patch_failure_garbage = [
+  same_file;
+  diff_file;
+]
+let diff_patch_failure_garbage =
+  "something in\n" ^
+  "the file\n" ^
+  "that is not\n" ^
+  "patch format\n"
+
+let content_patch_failure_truncated = [
+  same_file;
+  diff_file;
+  diff_file_plus_fst;
+]
+let diff_patch_failure_truncated =
+  "--- first/diff-file\n" ^
+  "+++ second/diff-file\n" ^
+  "@@ -1,1 +1,1 @@\n" ^
+  "-foo\n" ^
+  "+bar\n" ^
+  "--- first/diff-fi\n"
+
+let _good_diff =
+  "\n" ^
+  "--- first/diff-file\n" ^
+  "+++ second/diff-file\n" ^
+  "@@ -1,1 +1,1 @@\n" ^
+  "-foo\n" ^
+  "+bar\n" ^
+  "--- first/diff-file-plus-fst\n" ^
+  "+++ second/diff-file-plus-fst\n" ^
+  "@@ -2,1 +2,0 @@\n" ^
+  "-bar\n"
+
+(** Utils *)
+
+let print = Printf.printf
+
+open OpamFilename.Op
+let read_dir root names =
+  let lst =
+    List.map (fun name ->
+        let dir = root / name in
+        (name^"/", []) ::
+        List.map (fun f ->
+            OpamFilename.remove_prefix root f,
+            OpamStd.String.split (OpamFilename.read f) '\n')
+          (OpamFilename.rec_files dir)
+        @
+        List.map (fun d -> OpamFilename.remove_prefix_dir root d, [])
+          (OpamFilename.rec_dirs dir))
+      names
+    |> List.flatten
+    |> List.map (fun (file, content) ->
+        (OpamSystem.back_to_forward file, content))
+  in
+
+  let lst = List.sort (fun (f,_) (f',_) -> String.compare f f') lst in
+  OpamStd.Format.itemize ~bullet:"+ "
+    (function
+      | d, [] -> d
+      | d, c ->
+        Printf.sprintf "%s\n%s"
+          d
+          (OpamStd.List.concat_map ~left:"" ~right:"" "\n"
+             (Printf.sprintf "> %s") c))
+    lst
+
+let first = "first"
+let second = "second"
+
+let write_setup dir content =
+  let first_root = dir / first in
+  let second_root = dir / second in
+  List.iter (fun d ->
+      OpamFilename.cleandir d;
+      OpamFilename.mkdir d)
+    [ first_root; second_root; ] ;
+  let link_f =
+    let link = lazy (
+      let f = dir // "linked_file" in
+      if not (OpamFilename.exists f) then
+        OpamFilename.write f bar;
+      f
+    ) in
+    fun () -> Lazy.force link
+  in
+  let create inner_dir name = function
+    | File content ->
+      OpamFilename.write (inner_dir // name) content
+    | Dir lst ->
+      let inner_dir = inner_dir / name in
+      List.iter (fun (n,c) -> OpamFilename.write (inner_dir // n) c) lst
+    | Symlink ->
+      OpamFilename.link ~relative:false ~target:(link_f ())
+        ~link:(inner_dir // name)
+    | Hardlink ->
+      let target = OpamFilename.to_string (link_f ()) in
+      let link = OpamFilename.to_string (inner_dir // name) in
+      Unix.link target link
+    | V -> ()
+  in
+  List.iter (fun {name; first; second} ->
+      create first_root name first;
+      create second_root name second)
+    content
+
+type diff_patch =
+  | DiffPatch
+  | Patch of string
+
+let print_dirs dir =
+  print "%s\n" (read_dir dir [ first; second ])
+
+let diff_patch dir content kind =
+  write_setup dir content;
+  print "*** SETUP ***\n";
+  print_dirs dir;
+  let diff =
+    match kind with
+    | Patch patch ->
+      print "*** GIVEN DIFF ***\n";
+      let fpatch = dir // "patch" in
+      OpamFilename.write fpatch patch;
+      Some fpatch
+    | DiffPatch ->
+      print "*** DIFF ***\n";
+      match
+        OpamRepositoryBackend.get_diff dir
+          (OpamFilename.Base.of_string first)
+          (OpamFilename.Base.of_string second)
+      with
+      | exception Failure s -> print "ERROR: %s\n" s; None
+      | None -> print "No diff\n"; None
+      | some -> some
+  in
+  match diff with
+  | None -> ()
+  | Some diff ->
+    print "%s\n" (OpamFilename.read diff);
+    let result =
+      OpamFilename.patch ~allow_unclean:false diff
+        (dir / first)
+    in
+    match result with
+    | None ->
+      print "*** PATCHED ***\n";
+      print_dirs dir
+    | Some exn ->
+      print "*** PATCH ERROR ***\n";
+      print "ERROR: %s\n" (Printexc.to_string exn)
+
+(** The tests *)
+
+let tests = [
+  "normal", content_working_diff, DiffPatch;
+  "diff file/dir error", content_dir_file, DiffPatch;
+  "diff dir/file error", content_file_dir, DiffPatch;
+  "symlink fst", content_symlink_fst, DiffPatch;
+  "symlink snd", content_symlink_snd, DiffPatch;
+  "hardlink fst", content_hardlink_fst, DiffPatch;
+  "hardlink snd", content_hardlink_snd, DiffPatch;
+  "patch error garbage", content_patch_failure_garbage,
+  Patch diff_patch_failure_garbage;
+  "patch truncated", content_patch_failure_truncated,
+  Patch diff_patch_failure_truncated;
+]
+
+let () =
+  (* This causes Windows to use LF endings instead of CRLF, which simplifies the comparison with the reference file *)
+  Unix.putenv "LC_ALL" "C";
+  set_binary_mode_out stdout true;
+  Unix.dup2 Unix.stdout Unix.stderr;
+  OpamFilename.with_tmp_dir @@ fun dir ->
+  List.iteri (fun i (label, content, kind) ->
+      print "\n----------------------\n";
+      print " Test %d: %s\n" (i+1) label;
+      print "----------------------\n\n";
+      diff_patch dir content kind)
+    tests