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-29.3/src/comp.c
===================================================================
--- emacs-29.3.orig/src/comp.c
+++ emacs-29.3/src/comp.c
@@ -805,7 +805,7 @@ hash_native_abi (void)
   Vcomp_abi_hash =
     comp_hash_string (
       concat3 (build_string (ABI_VERSION),
-	       concat3 (Vemacs_version, Vsystem_configuration,
+	       concat2 (Vsystem_configuration,
 			Vsystem_configuration_options),
 	       Fmapconcat (intern_c_string ("comp--subr-signature"),
 			   Vcomp_subr_list, build_string (""))));
@@ -835,8 +835,7 @@ hash_native_abi (void)
     }
 #endif
 
-  Vcomp_native_version_dir =
-    concat3 (version, build_string ("-"), Vcomp_abi_hash);
+  Vcomp_native_version_dir = Vcomp_abi_hash;
 }
 
 static void
@@ -4396,26 +4395,17 @@ 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 +4414,55 @@ 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);
-
-  if (suffix_p (filename, ".gz"))
-    filename = Fsubstring (filename, Qnil, make_fixnum (-3));
-
-  /* We create eln filenames with an hash in order to look-up these
-     starting from the source filename, IOW have a relation
-
-     /absolute/path/filename.el + content ->
-     eln-cache/filename-path_hash-content_hash.eln.
-
-     '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 (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));
-    }
+  Lisp_Object tail = Vload_path;
+  Lisp_Object name_len = Flength (filename);
 
-  Lisp_Object lds_re_tail = loadsearch_re_list;
-  FOR_EACH_TAIL (lds_re_tail)
+  FOR_EACH_TAIL_SAFE (tail)
     {
-      Lisp_Object match_idx =
-	Fstring_match (XCAR (lds_re_tail), filename, Qnil, Qnil);
-      if (BASE_EQ (match_idx, make_fixnum (0)))
+      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 =
-	    Freplace_match (build_string ("//"), Qt, Qt, filename, Qnil);
+	  filename = Fsubstring (filename, len, 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));
+
+  if (file_name_absolute_p (filename)) /* no match in load-path */
+    filename = rel_name;
+
+  Lisp_Object bogus_dirs =
+    Fgetenv_internal (build_string ("NATIVE_COMP_BOGUS_DIRS"), Qnil);
+
+  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 (suffix_p (filename, ".gz"))
+    filename = Fsubstring (filename, Qnil, make_fixnum (-3));
+
+  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 +4476,7 @@ 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;
@@ -4548,10 +4524,11 @@ the latter is supposed to be used by the
   Lisp_Object lisp_preloaded =
     Fgetenv_internal (build_string ("LISP_PRELOADED"), Qnil);
   base_dir = Fexpand_file_name (Vcomp_native_version_dir, base_dir);
+  bool preloaded = comp_file_preloaded_p;
   if (comp_file_preloaded_p
       || (!NILP (lisp_preloaded)
-	  && !NILP (Fmember (CALL1I (file-name-base, source_filename),
-			     Fmapcar (intern_c_string ("file-name-base"),
+	  && !NILP (Fmember (CALL1I (file-name-sans-extension, source_filename),
+			     Fmapcar (intern_c_string ("file-name-sans-extension"),
 				      CALL1I (split-string, lisp_preloaded))))))
     base_dir = Fexpand_file_name (build_string ("preloaded"), base_dir);
 
@@ -5863,10 +5840,7 @@ 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/lisp/loadup.el
===================================================================
--- emacs-29.2.orig/lisp/loadup.el
+++ emacs-29.2/lisp/loadup.el
@@ -53,6 +53,14 @@
 (setq redisplay--inhibit-bidi t)
 
 (message "Dump mode: %s" dump-mode)
+;; Compensate for native-comp-eln-load-path being empty by Guix' default.
+(and (featurep 'native-compile)
+     dump-mode
+     (setq
+      native-comp-eln-load-path
+      (cons (expand-file-name "../native-lisp" invocation-directory)
+            native-comp-eln-load-path)
+      comp-file-preloaded-p t))
 
 ;; Add subdirectories to the load-path for files that might get
 ;; autoloaded when bootstrapping or running Emacs normally.
@@ -494,22 +502,20 @@ lost after dumping")))
             (concat eln-dest-dir "native-lisp/" comp-native-version-dir "/"))
       (maphash (lambda (_ cu)
                  (let* ((file (native-comp-unit-file cu))
-                        (preloaded (equal (substring (file-name-directory file)
-                                                     -10 -1)
-                                          "preloaded"))
-                        (eln-dest-dir-eff (if preloaded
-                                              (expand-file-name "preloaded"
-                                                                eln-dest-dir)
-                                            eln-dest-dir)))
+                        (native-lisp-needle
+                         (regexp-quote (concat "native-lisp/"
+                                               comp-native-version-dir "/"))))
                    (native-comp-unit-set-file
                     cu
 	            (cons
                      ;; Relative filename from the installed binary.
-                     (file-relative-name (expand-file-name
-                                          (file-name-nondirectory
-                                           file)
-                                          eln-dest-dir-eff)
-                                         bin-dest-dir)
+                     (file-relative-name
+                      (expand-file-name
+                       (save-match-data
+                         (string-match native-lisp-needle file)
+                         (substring file (match-end 0)))
+                       eln-dest-dir)
+                      bin-dest-dir)
                      ;; Relative filename from the built uninstalled binary.
                      (file-relative-name file invocation-directory)))))
 	       comp-loaded-comp-units-h)))
@@ -557,7 +563,9 @@ lost after dumping")))
                  (equal dump-mode "pdump"))
         ;; Don't enable this before bootstrap is completed, as the
         ;; compiler infrastructure may not be usable yet.
-        (setq native-comp-enable-subr-trampolines t))
+        (setq native-comp-enable-subr-trampolines t
+              ;; We loaded everything we could.
+              comp-file-preloaded-p nil))
       (message "Dumping under the name %s" output)
       (condition-case ()
           (delete-file output)
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.