Since https://github.com/emacs-mirror/emacs/commit/370b216f08699bdd85b910868642df441c06306c
project-find-file will produce a list where files located in a git
submodule is listed relative to the submodule instead of relative to the
project root. The problem happens when recursing into submodules if
project--vc-merge-submodules-p is true. I managed to fix it locally by
concating the module name to the file in the recursive call:

    (let ((sub-files-maybe-relative
   (project--vc-list-files
    (concat default-directory module)
    backend
    extra-ignores)))
      (if project-files-relative-names
  ;; If project--vc-list-files returns relative names, then concat the submodule name
  (mapcar (lambda (file) (concat (file-name-as-directory module) file)) sub-files-maybe-relative)
                         sub-files-maybe-relative))

I don't know if this is the correct approach though.


In GNU Emacs 29.3 (build 1, aarch64-apple-darwin23.5.0, NS
 appkit-2487.60 Version 14.5 (Build 23F79)) of 2024-06-12 built on
 WRY7PK7266
Windowing system distributor 'Apple', version 10.3.2487
System Description:  macOS 14.5

Configured using:
 'configure --disable-dependency-tracking --disable-silent-rules
 --enable-locallisppath=/opt/homebrew/share/emacs/site-lisp
 --infodir=/opt/homebrew/Cellar/emacs-plus@29/29.3/share/info/emacs
 --prefix=/opt/homebrew/Cellar/emacs-plus@29/29.3 --with-xml2
 --with-gnutls --without-compress-install --without-dbus
 --without-imagemagick --with-modules --with-rsvg --with-ns
 --disable-ns-self-contained 'CFLAGS=-Os -w -pipe
 -mmacosx-version-min=14
 -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk
 -DFD_SETSIZE=10000 -DDARWIN_UNLIMITED_SELECT'
 'CPPFLAGS=-I/opt/homebrew/opt/icu4c/include
 -I/opt/homebrew/opt/sqlite/include -I/opt/homebrew/opt/readline/include
 -isystem/opt/homebrew/include -F/opt/homebrew/Frameworks
 -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk'
 'LDFLAGS=-L/opt/homebrew/opt/icu4c/lib -L/opt/homebrew/opt/sqlite/lib
 -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/lib
 -F/opt/homebrew/Frameworks -Wl,-headerpad_max_install_names
 -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk''

Configured features:
ACL GIF GLIB GMP GNUTLS JPEG JSON LCMS2 LIBXML2 MODULES NOTIFY KQUEUE NS
PDUMPER PNG RSVG SQLITE3 THREADS TIFF TOOLKIT_SCROLL_BARS TREE_SITTER
WEBP XIM ZLIB

Important settings:
  value of $LANG: en_US.UTF-8
  locale-coding-system: utf-8-unix

Major mode: ELisp/l

Minor modes in effect:
  tree-sitter-hl-mode: t
  global-tree-sitter-mode: t
  tree-sitter-mode: t
  marginalia-mode: t
  savehist-mode: t
  vertico-mode: t
  corfu-popupinfo-mode: t
  global-corfu-mode: t
  corfu-mode: t
  which-key-mode: t
  rainbow-delimiters-mode: t
  global-whitespace-mode: t
  doom-modeline-mode: t
  server-mode: t
  windmove-mode: t
  recentf-mode: t
  override-global-mode: t
  tooltip-mode: t
  global-eldoc-mode: t
  eldoc-mode: t
  show-paren-mode: t
  electric-indent-mode: t
  mouse-wheel-mode: t
  file-name-shadow-mode: t
  global-font-lock-mode: t
  font-lock-mode: t
  blink-cursor-mode: t
  line-number-mode: t
  indent-tabs-mode: t
  transient-mark-mode: t
  auto-composition-mode: t
  auto-encryption-mode: t
  auto-compression-mode: t

Load-path shadows:
/Users/bohrarper/.emacs.d/elpa/cmake-mode-20240412.1329/cmake-mode hides /opt/homebrew/share/emacs/site-lisp/cmake/cmake-mode
/Users/bohrarper/.emacs.d/elpa/protobuf-mode-20240222.1652/protobuf-mode hides /opt/homebrew/share/emacs/site-lisp/protobuf/protobuf-mode
/Users/bohrarper/.emacs.d/elpa/transient-20240609.2020/transient hides /opt/homebrew/Cellar/emacs-plus@29/29.3/share/emacs/29.3/lisp/transient
/Users/bohrarper/.emacs.d/elpa/jsonrpc-1.0.25/jsonrpc hides /opt/homebrew/Cellar/emacs-plus@29/29.3/share/emacs/29.3/lisp/jsonrpc
/Users/bohrarper/.emacs.d/elpa/use-package-20230426.2324/use-package-jump hides /opt/homebrew/Cellar/emacs-plus@29/29.3/share/emacs/29.3/lisp/use-package/use-package-jump
/Users/bohrarper/.emacs.d/elpa/use-package-20230426.2324/use-package-diminish hides /opt/homebrew/Cellar/emacs-plus@29/29.3/share/emacs/29.3/lisp/use-package/use-package-diminish
/Users/bohrarper/.emacs.d/elpa/use-package-20230426.2324/use-package hides /opt/homebrew/Cellar/emacs-plus@29/29.3/share/emacs/29.3/lisp/use-package/use-package
/Users/bohrarper/.emacs.d/elpa/use-package-20230426.2324/use-package-delight hides /opt/homebrew/Cellar/emacs-plus@29/29.3/share/emacs/29.3/lisp/use-package/use-package-delight
/Users/bohrarper/.emacs.d/elpa/use-package-20230426.2324/use-package-lint hides /opt/homebrew/Cellar/emacs-plus@29/29.3/share/emacs/29.3/lisp/use-package/use-package-lint
/Users/bohrarper/.emacs.d/elpa/bind-key-20230203.2004/bind-key hides /opt/homebrew/Cellar/emacs-plus@29/29.3/share/emacs/29.3/lisp/use-package/bind-key
/Users/bohrarper/.emacs.d/elpa/use-package-20230426.2324/use-package-core hides /opt/homebrew/Cellar/emacs-plus@29/29.3/share/emacs/29.3/lisp/use-package/use-package-core
/Users/bohrarper/.emacs.d/elpa/use-package-20230426.2324/use-package-ensure hides /opt/homebrew/Cellar/emacs-plus@29/29.3/share/emacs/29.3/lisp/use-package/use-package-ensure
/Users/bohrarper/.emacs.d/elpa/use-package-20230426.2324/use-package-bind-key hides /opt/homebrew/Cellar/emacs-plus@29/29.3/share/emacs/29.3/lisp/use-package/use-package-bind-key
/Users/bohrarper/.emacs.d/elpa/flymake-1.3.7/flymake hides /opt/homebrew/Cellar/emacs-plus@29/29.3/share/emacs/29.3/lisp/progmodes/flymake
/Users/bohrarper/.emacs.d/elpa/xref-1.7.0/xref hides /opt/homebrew/Cellar/emacs-plus@29/29.3/share/emacs/29.3/lisp/progmodes/xref
/Users/bohrarper/.emacs.d/elpa/project-0.11.0/project hides /opt/homebrew/Cellar/emacs-plus@29/29.3/share/emacs/29.3/lisp/progmodes/project
/Users/bohrarper/.emacs.d/elpa/eglot-1.17/eglot hides /opt/homebrew/Cellar/emacs-plus@29/29.3/share/emacs/29.3/lisp/progmodes/eglot
/Users/bohrarper/.emacs.d/elpa/eldoc-1.15.0/eldoc hides /opt/homebrew/Cellar/emacs-plus@29/29.3/share/emacs/29.3/lisp/emacs-lisp/eldoc

Features:
(shadow sort mail-extr emacsbug message puny rfc822 mml mml-sec epa
derived epg rfc6068 epg-config gnus-util mailabbrev gmm-utils mailheader
sendmail mail-utils misearch multi-isearch face-remap yank-media
markdown-mode noutline outline vc-git vc-dispatcher eglot
external-completion jsonrpc xref flymake thingatpt diff diff-mode ert
ewoc debug backtrace advice find-func filenotify warnings icons imenu
vertico-directory cc-mode cc-fonts cc-guess cc-menus cc-cmds cc-styles
cc-align cc-engine cc-vars cc-defs orderless cursor-sensor
vertico-repeat project consult bookmark pulse color persistent-soft
list-utils pcache eieio-base cl font-utils parse-time iso8601 time-date
tree-sitter-langs tree-sitter-langs-build tar-mode arc-mode archive-mode
pp tree-sitter-hl tree-sitter tree-sitter-load tree-sitter-cli tsc
tsc-dyn tsc-dyn-get compile text-property-search comint ansi-osc
ansi-color dired-aux dired dired-loaddefs tsc-obsolete marginalia
savehist vertico clang-format xml corfu-popupinfo corfu cus-load
which-key two-column hydra ring lv edmacro kmacro rainbow-delimiters
disp-table whitespace material-theme doom-modeline
doom-modeline-segments doom-modeline-env doom-modeline-core shrink-path
f s dash nerd-icons nerd-icons-faces nerd-icons-data
nerd-icons-data-mdicon nerd-icons-data-flicon nerd-icons-data-codicon
nerd-icons-data-devicon nerd-icons-data-sucicon nerd-icons-data-wicon
nerd-icons-data-faicon nerd-icons-data-powerline nerd-icons-data-octicon
nerd-icons-data-pomicon nerd-icons-data-ipsicon compat unicode-fonts
exec-path-from-shell delight server windmove recentf tree-widget
wid-edit quelpa-use-package quelpa mm-decode mm-bodies mm-encode
mail-parse rfc2231 rfc2047 rfc2045 mm-util ietf-drums mail-prsvr
lisp-mnt help-fns radix-tree cl-extra help-mode use-package
use-package-ensure use-package-delight use-package-diminish
use-package-bind-key bind-key easy-mmode use-package-core finder-inf
all-the-icons-completion-autoloads all-the-icons-autoloads
async-autoloads auto-compile-autoloads bazel-autoloads rx
blacken-autoloads cargo-autoloads clang-format-autoloads
cmake-mode-autoloads consult-autoloads copilot-autoloads
corfu-terminal-autoloads corfu-autoloads dart-mode-autoloads
doom-modeline-autoloads editorconfig-autoloads eglot-java-autoloads
eglot-autoloads exec-path-from-shell-autoloads expand-region-autoloads
flutter-autoloads flymake-autoloads eldoc-autoloads jsonrpc-autoloads
kind-icon-autoloads magit-autoloads pcase git-commit-autoloads
magit-section-autoloads marginalia-autoloads markdown-mode-autoloads
multiple-cursors-autoloads nerd-icons-autoloads orderless-autoloads
org-page-autoloads htmlize-autoloads prescient-autoloads
project-autoloads project-mode-line-tag-autoloads
protobuf-mode-autoloads quelpa-use-package-autoloads quelpa-autoloads
rust-mode-autoloads f-autoloads simple-httpd-autoloads svg-lib-autoloads
transient-autoloads tree-sitter-langs-autoloads tree-sitter-autoloads
treemacs-autoloads posframe-autoloads dash-autoloads tsc-autoloads
typescript-mode-autoloads unicode-fonts-autoloads vertico-autoloads
web-mode-autoloads which-key-autoloads with-editor-autoloads info
compat-autoloads xref-autoloads yaml-autoloads yaml-mode-autoloads
yasnippet-snippets-autoloads yasnippet-autoloads zig-mode-autoloads
reformatter-autoloads package browse-url url url-proxy url-privacy
url-expand url-methods url-history url-cookie generate-lisp-file
url-domsuf url-util mailcap url-handlers url-parse auth-source cl-seq
eieio eieio-core cl-macs password-cache json subr-x map byte-opt gv
bytecomp byte-compile url-vars cl-loaddefs cl-lib rmc iso-transl tooltip
cconv eldoc paren electric uniquify ediff-hook vc-hooks lisp-float-type
elisp-mode mwheel term/ns-win ns-win ucs-normalize mule-util
term/common-win tool-bar dnd fontset image regexp-opt fringe
tabulated-list replace newcomment text-mode lisp-mode prog-mode register
page tab-bar menu-bar rfn-eshadow isearch easymenu timer select
scroll-bar mouse jit-lock font-lock syntax font-core term/tty-colors
frame minibuffer nadvice seq simple cl-generic indonesian philippine
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 emoji-zwj charscript
charprop case-table epa-hook jka-cmpr-hook help abbrev obarray oclosure
cl-preloaded button loaddefs theme-loaddefs faces cus-face macroexp
files window text-properties overlay sha1 md5 base64 format env
code-pages mule custom widget keymap hashtable-print-readable backquote
threads kqueue cocoa ns lcms2 multi-tty make-network-process emacs)

Memory information:
((conses 16 495522 257431)
 (symbols 48 30607 3)
 (strings 32 172029 24046)
 (string-bytes 1 4360706)
 (vectors 16 48125)
 (vector-slots 8 670691 444580)
 (floats 8 359 1216)
 (intervals 56 3756 2278)
 (buffers 984 19))