bug#44066: 27.1; Values ignored when using .dir-locals.el and .dir-locals-2.el together

[Jacob First]

Hello,

I've experienced a case where some directory local variable values are
ignored when .dir-locals.el and .dir-locals-2.el are both present in a
directory. As Emacs normally sets all the variable values when only one
of the files is present, and I can find nothing in the manual to suggest
that the behavior should be different when both are present, I believe
this behavior is erroneous.

To reproduce, first create a directory with 3 files with the filenames
and the contents listed below:

= file.txt =
test file

= .dir-locals.el =
((nil . ((eval . (setq var1 'foo)) (eval . (setq var2 'bar)))))

= .dir-locals-2.el =
((nil . ((eval . (setq var3 'baz)) (eval . (setq var4 'qux)))))

Then run:

    emacs -Q file.txt

Emacs should display a prompt with a message beginning "The local
variables list in /path/to/the/dir/ contains values that may not be safe
(*)" with a list of potentially unsafe values at the bottom.

I expect to see the following values listed in some order:

  * eval : (setq var1 'foo)
  * eval : (setq var2 'bar)
  * eval : (setq var3 'baz)
  * eval : (setq var4 'qux)

Instead, only the following values are listed:

  * eval : (setq var4 'qux)
  * eval : (setq var2 'bar)

If I then type ! to accept the values, evaluating each variable via M-:
will confirm that only var2 and var4 have been set and that var1 and
var3 are unbound.

If I quit Emacs, delete .dir-locals-2.el, and follow the above steps
again, the prompt now lists all the values from .dir-locals.el as
expected:

  * eval : (setq var1 'foo)
  * eval : (setq var2 'bar)

Similarly if I delete .dir-locals.el but keep .dir-locals-2.el intact,
the prompt lists all the values from .dir-locals-2.el as expected:

  * eval : (setq var3 'baz)
  * eval : (setq var4 'qux)

Autogenerated system info follows. Thank you.

***

In GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.20, cairo 
version 1.16.0)
Windowing system distributor 'The X.Org Foundation', version 11.0.12009000
Recent messages:
For information about GNU Emacs and the GNU system, type C-h C-a.
End of buffer [3 times]
Please type y, n, or !, or C-v/M-v to scroll: !
Setting ‘safe-local-variable-values’ temporarily since "emacs -q" would 
overwrite customizations

Configured using:
 'configure
 
CONFIG_SHELL=/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash
 SHELL=/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash
 --prefix=/gnu/store/zcrrjwkzzlx96szsxmacflrl3bybm413-emacs-27.1
 --enable-fast-install --with-modules --with-cairo
 --disable-build-details'

Configured features:
XPM JPEG TIFF GIF PNG RSVG CAIRO SOUND DBUS GSETTINGS GLIB NOTIFY
INOTIFY ACL LIBSELINUX GNUTLS LIBXML2 FREETYPE HARFBUZZ M17N_FLT LIBOTF
ZLIB TOOLKIT_SCROLL_BARS GTK3 X11 XDBE XIM MODULES THREADS JSON PDUMPER
GMP

Important settings:
  value of $EMACSLOADPATH: 
/home/jfirst/.local/share/guix/extra-profiles/gui/gui/share/emacs/27.1/lisp:/home/jfirst/.local/share/guix/extra-profiles/gui/gui/share/emacs/site-lisp
  value of $LANG: en_US.utf8
  locale-coding-system: utf-8-unix

Major mode: Text

Minor modes in effect:
  tooltip-mode: t
  global-eldoc-mode: t
  electric-indent-mode: t
  mouse-wheel-mode: t
  tool-bar-mode: t
  menu-bar-mode: t
  file-name-shadow-mode: t
  global-font-lock-mode: t
  font-lock-mode: t
  blink-cursor-mode: t
  auto-composition-mode: t
  auto-encryption-mode: t
  auto-compression-mode: t
  line-number-mode: t
  transient-mark-mode: t

Load-path shadows:
None found.

Features:
(shadow sort mail-extr emacsbug message rmc puny dired dired-loaddefs
format-spec rfc822 mml mml-sec password-cache epa derived epg epg-config
gnus-util rmail rmail-loaddefs text-property-search time-date subr-x
mm-decode mm-bodies mm-encode mail-parse rfc2231 mailabbrev gmm-utils
mailheader sendmail rfc2047 rfc2045 ietf-drums mm-util mail-prsvr
mail-utils cus-edit easymenu cus-start cus-load wid-edit cl-loaddefs
cl-lib map seq byte-opt gv bytecomp byte-compile cconv tooltip eldoc
electric uniquify ediff-hook vc-hooks lisp-float-type mwheel term/x-win
x-win term/common-win x-dnd tool-bar dnd fontset image regexp-opt fringe
tabulated-list replace newcomment text-mode elisp-mode lisp-mode
prog-mode register page tab-bar menu-bar rfn-eshadow isearch timer
select scroll-bar mouse jit-lock font-lock syntax facemenu font-core
term/tty-colors frame minibuffer cl-generic cham georgian utf-8-lang
misc-lang vietnamese tibetan thai tai-viet lao korean japanese eucjp-ms
cp51932 hebrew greek romanian slovak czech european ethiopic indian
cyrillic chinese composite charscript charprop case-table epa-hook
jka-cmpr-hook help simple abbrev obarray cl-preloaded nadvice loaddefs
button faces cus-face macroexp files text-properties overlay sha1 md5
base64 format env code-pages mule custom widget hashtable-print-readable
backquote threads dbusbind inotify dynamic-setting system-font-setting
font-render-setting cairo move-toolbar gtk x-toolkit x multi-tty
make-network-process emacs)

Memory information:
((conses 16 66357 9862)
 (symbols 48 7546 1)
 (strings 32 20201 1623)
 (string-bytes 1 628515)
 (vectors 16 10568)
 (vector-slots 8 138494 9480)
 (floats 8 29 23)
 (intervals 56 194 0)
 (buffers 1000 13))