[BUG] Questionmarks in org-agenda instead of file names [9.5.2 (9.5.2-g3154c2 @ /Users/eugr/.emacs.d/straight/build/org/)]

[Eugene Rakhmatulin <eugr@eugr.com>]

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Remember to cover the basics, that is, what you expected to happen and
what in fact did happen.  You don't know how to make a good report?  See

     https://orgmode.org/manual/Feedback.html#Feedback

Your bug report will be posted to the Org mailing list.
------------------------------------------------------------------------

When any of the agenda files get updated outside of this instance of
Emacs (e.g. another editor or in my case Emacs on another machine via a
synced iCloud Drive folder), questionmarks are displayed instead of a
file name. That does not always happen, but when it happens, the only
way to get rid of the questionmarks is to go to the offending file buffer
and
run org-element-cache-reset on that buffer. Just rebuilding the agenda
doesn't help, and even restarting Emacs doesn't help.

After the cache is reset, everything works as expected.

Org is built from main/master branch. It shows 9.5.2 but I see 9.6-dev
in the source files headers. This is Emacs 27.2 (Yamamoto Mituharu
port), but this also happens on 28.0.90 built from the source on my
other Mac. I tried with both Doom and (in this case) vanilla Emacs with
hand-picked packages loaded.

Emacs  : GNU Emacs 27.2 (build 1, aarch64-apple-darwin21.2.0, Carbon
Version 165 AppKit 2113.2)
of 2021-12-27
Package: Org mode version 9.5.2 (9.5.2-g3154c2 @
/Users/eugr/.emacs.d/straight/build/org/)

current state:
==============
(setq
org-src-mode-hook '(doom-modeline-set-org-src-modeline
org-src-babel-configure-edit-buffer
    org-src-mode-configure-edit-buffer)
org-fontify-whole-heading-line t
org-link-shell-confirm-function 'yes-or-no-p
org-metadown-hook '(org-babel-pop-to-session-maybe)
org-refile-targets '((nil :maxlevel . 3) (org-agenda-files :maxlevel . 3))
org-enforce-todo-dependencies t
org-imenu-depth 6
org-persist-before-write-hook '(org-element--cache-persist-before-write)
org-agenda-files '("~/org/")
org-log-redeadline 'note
org-startup-folded nil
org-blocker-hook '(org-block-todo-from-children-or-siblings-or-parent)
org-super-agenda-mode t
org-mode-hook '((lambda nil (define-key org-mode-map (kbd "C-c g")
'org-mac-grab-link))
#[0 "\301\211\207" [imenu-create-index-function org-imenu-get-tree] 2]
(lambda nil (org-superstar-mode 1)) visual-line-mode
#[0 "\300\301\302\303\304$\207" [add-hook change-major-mode-hook
org-show-all append local] 5]
#[0 "\300\301\302\303\304$\207"
  [add-hook change-major-mode-hook org-babel-show-result-all append local]
5]
org-babel-result-hide-spec org-babel-hide-all-hashes org-eldoc-load)
org-outline-path-complete-in-steps nil
org-archive-hook '(org-attach-archive-delete-maybe)
org-persist-before-read-hook '(org-element--cache-persist-before-read)
org-superstar-headline-bullets-list '("⁖" "◉" "○" "✸" "✿")
org-confirm-elisp-link-function 'yes-or-no-p
org-startup-indented t
org-startup-with-inline-images t
org-agenda-before-write-hook '(org-agenda-add-entry-text)
org-metaup-hook '(org-babel-load-in-session-maybe)
org-persist-after-read-hook '(org-element--cache-persist-after-read)
org-bibtex-headline-format-function #[257 "\300\236A\207" [:title] 3
"\n\n(fn ENTRY)"]
org-log-reschedule 'time
org-babel-pre-tangle-hook '(save-buffer)
org-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
org-hide-leading-stars t
org-babel-load-languages '((python . t) (shell . t))
org-log-done 'time
org-font-lock-hook '(org-inlinetask-fontify)
org-agenda-span 'day
org-agenda-loop-over-headlines-in-active-region nil
org-src-lang-modes '(("redis" . redis) ("php" . php) ("arduino" . arduino)
("C" . c) ("C++" . c++)
     ("asymptote" . asy) ("bash" . sh) ("beamer" . latex) ("calc" .
fundamental) ("cpp" . c++)
     ("ditaa" . artist) ("dot" . fundamental) ("elisp" . emacs-lisp)
("ocaml" . tuareg)
     ("screen" . shell-script) ("shell" . sh) ("sqlite" . sql))
org-fontify-quote-and-verse-blocks t
org-occur-hook '(org-first-headline-recenter)
org-agenda-window-setup 'current-window
org-log-into-drawer t
org-mac-grab-devonthink-app-p nil
org-indirect-buffer-display 'current-window
org-cycle-hook '(org-inlinetask-hide-tasks org-cycle-hide-archived-subtrees
org-cycle-hide-drawers
 org-cycle-show-empty-lines org-optimize-window-after-visibility-change)
org-todo-keywords '((sequence "TODO(t)" "PROJ(p)" "LOOP(r)" "STRT(s)"
"WAIT(w@/!)" "HOLD(h@/!)" "IDEA(i)" "|"
     "DONE(d)" "KILL(k@)")
    )
org-speed-command-hook '(org-speed-command-activate
org-babel-speed-command-activate)
org-tags-column 0
org-babel-tangle-lang-exts '(("python" . "py") ("emacs-lisp" . "el")
("elisp" . "el"))
org-refile-use-outline-path 'file
org-priority-faces '((65 . error) (66 . warning) (67 . success))
org-export-before-parsing-hook '(org-attach-expand-links)
org-confirm-shell-link-function 'yes-or-no-p
org-link-parameters '(("attachment" :follow org-attach-follow :complete
org-attach-complete-link)
      ("eww" :follow org-eww-open :store org-eww-store-link)
      ("rmail" :follow org-rmail-open :store org-rmail-store-link)
      ("mhe" :follow org-mhe-open :store org-mhe-store-link)
      ("irc" :follow org-irc-visit :store org-irc-store-link :export
org-irc-export)
      ("info" :follow org-info-open :export org-info-export :store
org-info-store-link)
      ("gnus" :follow org-gnus-open :store org-gnus-store-link)
      ("docview" :follow org-docview-open :export org-docview-export :store
org-docview-store-link)
      ("bibtex" :follow org-bibtex-open :store org-bibtex-store-link)
      ("bbdb" :follow org-bbdb-open :export org-bbdb-export :complete
org-bbdb-complete-link
:store org-bbdb-store-link)
      ("w3m" :store org-w3m-store-link)
      ("doi" :follow org-link-doi-open :export org-link-doi-export)
      ("message" :follow org-mac-message-open)
      ("x-devonthink-item" :follow org-devonthink-item-open)
      ("mac-evernote" :follow org-mac-evernote-note-open)
      ("mac-outlook" :follow org-mac-outlook-message-open)
      ("acrobat" :follow org-mac-acrobat-open) ("skim" :follow
org-mac-skim-open)
      ("addressbook" :follow org-mac-addressbook-item-open)
      ("x-together-item" :follow org-mac-together-item-open) ("id" :follow
org-id-open)
      ("file+sys") ("file+emacs") ("shell" :follow org-link--open-shell)
      ("news" :follow
#[514 "\301\300\302Q\"\207" ["news" browse-url ":"] 6 "\n\n(fn URL ARG)"])
      ("mailto" :follow
#[514 "\301\300\302Q\"\207" ["mailto" browse-url ":"] 6 "\n\n(fn URL ARG)"])
      ("https" :follow
#[514 "\301\300\302Q\"\207" ["https" browse-url ":"] 6 "\n\n(fn URL ARG)"])
      ("http" :follow
#[514 "\301\300\302Q\"\207" ["http" browse-url ":"] 6 "\n\n(fn URL ARG)"])
      ("ftp" :follow #[514 "\301\300\302Q\"\207" ["ftp" browse-url ":"] 6
"\n\n(fn URL ARG)"])
      ("help" :follow org-link--open-help :store org-link--store-help)
      ("file" :complete org-link-complete-file) ("elisp" :follow
org-link--open-elisp))
org-link-elisp-confirm-function 'yes-or-no-p
org-todo-keyword-faces '(("STRT" . +org-todo-active) ("IDEA" .
+org-todo-onhold) ("WAIT" . +org-todo-onhold)
 ("HOLD" . +org-todo-onhold) ("PROJ" . +org-todo-project) ("KILL" .
+org-todo-cancel))
org-super-agenda-groups '((:name "Deadline today" :deadline today :order 0)
  (:name "Important" :priority "A" :order 1)
  (:name "Deadline <= 30d" :deadline (before "+31d") :order 9)
  (:name "Deadline > 30d" :and (:deadline (after "+30d") :not (:scheduled
today)) :order
   10)
  (:name "Waiting" :todo "WAIT" :order 8) (:name "On Hold" :todo "HOLD"
:order 9)
  (:name "Ideas" :todo "IDEA" :order 11) (:priority "B" :order 2)
  (:name "Next" :time-grid t :todo ("TODO" "STRT" "WAIT") :order 3))
org-image-actual-width nil
org-eldoc-breadcrumb-separator " → "
org-entities-user '(("flat" "\\flat" nil "" "" "266D" "♭") ("sharp"
"\\sharp" nil "" "" "266F" "♯"))
org-use-sub-superscripts '{}
org-agenda-todo-ignore-deadlines 'near
org-directory "~/org/"
org-agenda-todo-ignore-scheduled 'all
org-agenda-start-on-weekday nil
)

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