Upstream hashes both the absolute file name and the content of a file
to derive the name for the natively compiled files.  This breaks the
staged install used in guix, as any $GUIX_PROFILE is distinct from
the build directory.  It also breaks grafts, as hardcoded store file
names get rewritten; thus changing the file hash.

In addition, this patch changes how native-comp-eln-load-path is
constructed.  Upstream, an entry of the directory “../lisp” is added
supposedly for bootstrap only, but this directory appears to find its
way into the actual variable despite attempts to remove it by calling
‘startup--update-eln-cache’.
The user-visible procedure ‘startup-redirect-eln-cache’ is kept, as
packages may require it, but only pushes the new value now.

Index: emacs-29.2/src/comp.c
===================================================================
--- emacs-29.2.orig/src/comp.c
+++ emacs-29.2/src/comp.c
@@ -4396,26 +4396,17 @@ DEFUN ("comp-el-to-eln-rel-filename", Fc
        Scomp_el_to_eln_rel_filename, 1, 1, 0,
        doc: /* Return the relative name of the .eln file for FILENAME.
 FILENAME must exist, and if it's a symlink, the target must exist.
-If FILENAME is compressed, it must have the \".gz\" extension,
-and Emacs must have been compiled with zlib; the file will be
-uncompressed on the fly to hash its contents.
-Value includes the original base name, followed by 2 hash values,
-one for the file name and another for its contents, followed by .eln.  */)
+FILENAME is resolved relative to `load-path' and only the suffix of
+the first matching path is kept.  If FILENAME is not found to be relative
+to any directory `load-path', it is used as-is to construct the return
+value.  */)
   (Lisp_Object filename)
 {
   CHECK_STRING (filename);
 
-  /* Resolve possible symlinks in FILENAME, so that path_hash below
-     always compares equal. (Bug#44701).  */
-  filename = Fexpand_file_name (filename, Qnil);
-  char *file_normalized = realpath (SSDATA (ENCODE_FILE (filename)), NULL);
-  if (file_normalized)
-    {
-      filename = DECODE_FILE (make_unibyte_string (file_normalized,
-						   strlen (file_normalized)));
-      xfree (file_normalized);
-    }
+  Lisp_Object rel_name = filename;
 
+  filename = Fexpand_file_name (filename, Qnil);
   if (NILP (Ffile_exists_p (filename)))
     xsignal1 (Qfile_missing, filename);
 
@@ -4423,64 +4414,54 @@ one for the file name and another for it
   filename = Fw32_long_file_name (filename);
 #endif
 
-  Lisp_Object content_hash = comp_hash_source_file (filename);
+  Lisp_Object tail = Vload_path;
+  Lisp_Object name_len = Flength (filename);
 
-  if (suffix_p (filename, ".gz"))
-    filename = Fsubstring (filename, Qnil, make_fixnum (-3));
+  FOR_EACH_TAIL_SAFE (tail)
+    {
+      Lisp_Object len = Flength (XCAR (tail));
+      if (XFIXNUM (name_len) < XFIXNUM (len))
+	continue;
+      else if (EQ (Qt, Fcompare_strings (filename, make_fixnum (0), len,
+					 XCAR (tail), make_fixnum (0), len,
+					 Qnil)))
+        {
+          filename = Fsubstring (filename, Fadd1 (len), Qnil);
+	  break;
+	}
+    }
 
-  /* We create eln filenames with an hash in order to look-up these
-     starting from the source filename, IOW have a relation
+  if (Ffile_name_absolute_p (filename))
+    filename = rel_name;
 
-     /absolute/path/filename.el + content ->
-     eln-cache/filename-path_hash-content_hash.eln.
+  Lisp_Object bogus_dirs =
+    Fgetenv_internal (build_string ("NATIVE_COMP_BOGUS_DIRS"), Qnil);
 
-     'dlopen' can return the same handle if two shared with the same
-     filename are loaded in two different times (even if the first was
-     deleted!).  To prevent this scenario the source file content is
-     included in the hashing algorithm.
-
-     As at any point in time no more then one file can exist with the
-     same filename, should be possible to clean up all
-     filename-path_hash-* except the most recent one (or the new one
-     being recompiled).
-
-     As installing .eln files compiled during the build changes their
-     absolute path we need an hashing mechanism that is not sensitive
-     to that.  For this we replace if match PATH_DUMPLOADSEARCH or
-     *PATH_REL_LOADSEARCH with '//' before computing the hash.  */
+  if (!NILP (bogus_dirs))
+  {
+    tail = CALL2I (split-string, bogus_dirs, build_string (":"));
+
+    FOR_EACH_TAIL_SAFE (tail)
+      {
+	Lisp_Object directory = Ffile_name_as_directory (XCAR (tail));
+	Lisp_Object len = Flength (directory);
+	if (XFIXNUM (name_len) < XFIXNUM (len))
+	  continue;
+	else if (EQ (Qt, Fcompare_strings (filename, make_fixnum (0), len,
+					   directory, make_fixnum (0), len,
+					   Qnil)))
+	  {
+	    filename = Fsubstring (filename, len, Qnil);
+	    break;
+	  }
+      }
+  }
 
-  if (NILP (loadsearch_re_list))
-    {
-      Lisp_Object sys_re =
-	concat2 (build_string ("\\`[[:ascii:]]+"),
-		 Fregexp_quote (build_string ("/" PATH_REL_LOADSEARCH "/")));
-      Lisp_Object dump_load_search =
-	Fexpand_file_name (build_string (PATH_DUMPLOADSEARCH "/"), Qnil);
-#ifdef WINDOWSNT
-      dump_load_search = Fw32_long_file_name (dump_load_search);
-#endif
-      loadsearch_re_list = list2 (sys_re, Fregexp_quote (dump_load_search));
-    }
+  if (suffix_p (filename, ".gz"))
+    filename = Fsubstring (filename, Qnil, make_fixnum (-3));
 
-  Lisp_Object lds_re_tail = loadsearch_re_list;
-  FOR_EACH_TAIL (lds_re_tail)
-    {
-      Lisp_Object match_idx =
-	Fstring_match (XCAR (lds_re_tail), filename, Qnil, Qnil);
-      if (BASE_EQ (match_idx, make_fixnum (0)))
-	{
-	  filename =
-	    Freplace_match (build_string ("//"), Qt, Qt, filename, Qnil);
-	  break;
-	}
-    }
-  Lisp_Object separator = build_string ("-");
-  Lisp_Object path_hash = comp_hash_string (filename);
-  filename = concat2 (Ffile_name_nondirectory (Fsubstring (filename, Qnil,
-							   make_fixnum (-3))),
-		      separator);
-  Lisp_Object hash = concat3 (path_hash, separator, content_hash);
-  return concat3 (filename, hash, build_string (NATIVE_ELISP_SUFFIX));
+  return concat2(Fsubstring (filename, Qnil, make_fixnum (-3)),
+		 build_string (NATIVE_ELISP_SUFFIX));
 }
 
 DEFUN ("comp-el-to-eln-filename", Fcomp_el_to_eln_filename,
@@ -4494,13 +4474,7 @@ If BASE-DIR is non-nil, use it as the di
 non-absolute BASE-DIR is interpreted as relative to `invocation-directory'.
 If BASE-DIR is omitted or nil, look for the first writable directory
 in `native-comp-eln-load-path', and use as BASE-DIR its subdirectory
-whose name is given by `comp-native-version-dir'.
-If FILENAME specifies a preloaded file, the directory for the .eln
-file is the \"preloaded/\" subdirectory of the directory determined
-as described above.  FILENAME is considered to be a preloaded file if
-the value of `comp-file-preloaded-p' is non-nil, or if FILENAME
-appears in the value of the environment variable LISP_PRELOADED;
-the latter is supposed to be used by the Emacs build procedure.  */)
+whose name is given by `comp-native-version-dir'. */)
   (Lisp_Object filename, Lisp_Object base_dir)
 {
   Lisp_Object source_filename = filename;
@@ -4541,19 +4515,7 @@ the latter is supposed to be used by the
 
   if (!file_name_absolute_p (SSDATA (base_dir)))
     base_dir = Fexpand_file_name (base_dir, Vinvocation_directory);
-
-  /* In case the file being compiled is found in 'LISP_PRELOADED' or
-     `comp-file-preloaded-p' is non-nil target for output the
-     'preloaded' subfolder.  */
-  Lisp_Object lisp_preloaded =
-    Fgetenv_internal (build_string ("LISP_PRELOADED"), Qnil);
   base_dir = Fexpand_file_name (Vcomp_native_version_dir, base_dir);
-  if (comp_file_preloaded_p
-      || (!NILP (lisp_preloaded)
-	  && !NILP (Fmember (CALL1I (file-name-base, source_filename),
-			     Fmapcar (intern_c_string ("file-name-base"),
-				      CALL1I (split-string, lisp_preloaded))))))
-    base_dir = Fexpand_file_name (build_string ("preloaded"), base_dir);
 
   return Fexpand_file_name (filename, base_dir);
 }
@@ -5859,10 +5821,7 @@ The last directory of this list is assum
 the system *.eln files, which are the files produced when building
 Emacs.  */);
 
-  /* Temporary value in use for bootstrap.  We can't do better as
-     `invocation-directory' is still unset, will be fixed up during
-     dump reload.  */
-  Vnative_comp_eln_load_path = Fcons (build_string ("../native-lisp/"), Qnil);
+  Vnative_comp_eln_load_path = Qnil;
 
   DEFVAR_LISP ("native-comp-enable-subr-trampolines",
 	       Vnative_comp_enable_subr_trampolines,
Index: emacs-29.2/lisp/startup.el
===================================================================
--- emacs-29.2.orig/lisp/startup.el
+++ emacs-29.2/lisp/startup.el
@@ -545,9 +545,6 @@ DIRS are relative."
 (defvar native-comp-jit-compilation)
 (defvar native-comp-enable-subr-trampolines)
 
-(defvar startup--original-eln-load-path nil
-  "Original value of `native-comp-eln-load-path'.")
-
 (defun startup-redirect-eln-cache (cache-directory)
   "Redirect the user's eln-cache directory to CACHE-DIRECTORY.
 CACHE-DIRECTORY must be a single directory, a string.
@@ -558,22 +555,10 @@ to `user-emacs-directory'.
 For best results, call this function in your early-init file,
 so that the rest of initialization and package loading uses
 the updated value."
-  ;; Remove the original eln-cache.
-  (setq native-comp-eln-load-path (cdr native-comp-eln-load-path))
-  ;; Add the new eln-cache.
   (push (expand-file-name (file-name-as-directory cache-directory)
                           user-emacs-directory)
         native-comp-eln-load-path))
 
-(defun startup--update-eln-cache ()
-  "Update the user eln-cache directory due to user customizations."
-  ;; Don't override user customizations!
-  (when (equal native-comp-eln-load-path
-               startup--original-eln-load-path)
-    (startup-redirect-eln-cache "eln-cache")
-    (setq startup--original-eln-load-path
-          (copy-sequence native-comp-eln-load-path))))
-
 (defun normal-top-level ()
   "Emacs calls this function when it first starts up.
 It sets `command-line-processed', processes the command-line,
@@ -1362,12 +1347,6 @@ please check its value")
       startup-init-directory)))
   (setq early-init-file user-init-file)
 
-  ;; Amend `native-comp-eln-load-path', since the early-init file may
-  ;; have altered `user-emacs-directory' and/or changed the eln-cache
-  ;; directory.
-  (when (featurep 'native-compile)
-    (startup--update-eln-cache))
-
   ;; If any package directory exists, initialize the package system.
   (and user-init-file
        package-enable-at-startup
@@ -1502,12 +1481,6 @@ please check its value")
         startup-init-directory))
      t)
 
-    ;; Amend `native-comp-eln-load-path' again, since the early-init
-    ;; file may have altered `user-emacs-directory' and/or changed the
-    ;; eln-cache directory.
-    (when (featurep 'native-compile)
-      (startup--update-eln-cache))
-
     (when (and deactivate-mark transient-mark-mode)
       (with-current-buffer (window-buffer)
         (deactivate-mark)))
Index: emacs-29.2/src/Makefile.in
===================================================================
--- emacs-29.2.orig/src/Makefile.in
+++ emacs-29.2/src/Makefile.in
@@ -553,6 +553,7 @@ shortlisp := $(filter-out ${shortlisp_fi
 ## We don't really need to sort, but may as well use it to remove duplicates.
 shortlisp := loaddefs.el loadup.el $(sort ${shortlisp})
 export LISP_PRELOADED = ${shortlisp}
+export NATIVE_COMP_BOGUS_DIRS
 lisp = $(addprefix ${lispsource}/,${shortlisp})
 
 ## Construct full set of libraries to be linked.
Index: emacs-29.2/Makefile.in
===================================================================
--- emacs-29.2.orig/Makefile.in
+++ emacs-29.2/Makefile.in
@@ -329,6 +329,7 @@ TRANSFORM = @program_transform_name@
 
 # Prevent any settings in the user environment causing problems.
 unexport EMACSDATA EMACSDOC EMACSLOADPATH EMACSPATH
+export EMACSNATIVELOADPATH = @abs_top_builddir@/native-lisp
 
 # What emacs should be called when installed.
 EMACS_NAME = `echo emacs | sed '$(TRANSFORM)'`