[BUG] query-replace breaks org-mode [9.6.6 (release_9.6.6 @ /Applications/Emacs.app/Contents/Resources/lisp/org/)]

[Joe Gilder <joe@homestudiocorner.com>]

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Noticed this a few times. When I run query-replace, it functions as usual. However, when I’m done with the query-replace, it seems to break org-fold. I can’t fold/unfold headings anymore. 

I had the same issue the other day with replace-string as well. 

Killing buffer and coming back fixes it. 

------------------------------------------------------------------------



Emacs  : GNU Emacs 29.1 (build 1, aarch64-apple-darwin21.6.0, Carbon Version 165 AppKit 2113.6)
 of 2023-08-08
Package: Org mode version 9.6.6 (release_9.6.6 @ /Applications/Emacs.app/Contents/Resources/lisp/org/)

current state:
==============
(setq
 org-agenda-prefix-format '((agenda . " %?-10t %s ") (timeline . "  % s")
			    (todo . " %s ") (tags . " %i ") (search . " %i %-12:c"))
 org-archive-location "~/Emacs/Archive.org::"
 org-log-note-headings '((note . "%t"))
 org-link-elisp-confirm-function nil
 org-agenda-skip-deadline-prewarning-if-scheduled t
 org-hide-emphasis-markers t
 org-bibtex-headline-format-function #[257 "\300\x01\236A\207" [:title] 3 "\n\n(fn ENTRY)"]
 org-download-file-format-function 'org-download-file-format-default
 org-attach-id-to-path-function-list '(org-attach-id-ts-folder-format)
 org-agenda-custom-commands '(("i" "INBOX + AGENDA"
			       ((todo "NEXT" ((org-agenda-overriding-header "Next"))
				 (org-agenda-skip-function
				  '(org-agenda-skip-entry-if 'date 'timestamp
				    'deadline 'scheduled)
				  )
				 (org-agenda-block-separator nil))
				(tags-todo "inbox"
				 ((org-agenda-overriding-header "Inbox")
				  (org-agenda-skip-function
				   '(org-agenda-skip-entry-if 'timestamp 'deadline
				     'scheduled 'todo
				     '("PROJECT" "NEXT" "WAITING" "DONE" "CANCELLED"))
				   )
				  (org-agenda-block-separator nil))
				 )
				(agenda "")
				(todo "PROJECT"
				 ((org-agenda-overriding-header "Projects")
				  (org-agenda-skip-function
				   '(org-agenda-skip-entry-if 'tags '("tickler")))
				  (org-agenda-block-separator 61))
				 )
				(tags-todo "@pam"
				 ((org-agenda-overriding-header "@Pam")
				  (org-agenda-block-separator 61)
				  (org-agenda-skip-function
				   '(org-agenda-skip-entry-if 'deadline 'scheduled
				     'todo
				     '("PROJECT" "NEXT" "WAITING" "DONE" "CANCELLED"))
				   )
				  )
				 )
				(tags-todo "@work"
				 ((org-agenda-overriding-header "@Work")
				  (org-agenda-block-separator nil)
				  (org-agenda-skip-function
				   '(org-agenda-skip-entry-if 'deadline 'scheduled
				     'todo
				     '("PROJECT" "NEXT" "WAITING" "DONE" "CANCELLED"))
				   )
				  )
				 )
				(tags-todo "@home"
				 ((org-agenda-overriding-header "@Home")
				  (org-agenda-block-separator nil)
				  (org-agenda-skip-function
				   '(org-agenda-skip-entry-if 'deadline 'scheduled
				     'todo
				     '("PROJECT" "NEXT" "WAITING" "DONE" "CANCELLED"))
				   )
				  )
				 )
				(todo "WAITING"
				 ((org-agenda-overriding-header "@Waiting/@Calendar")
				  (org-agenda-block-separator nil))
				 )
				)
			       )
			      )
 org-agenda-skip-scheduled-if-done t
 org-agenda-files '("~/Emacs/Todo.org" "~/Emacs/Journal.org" "~/Emacs/Notes.org"
		    "~/Emacs/.emacs.d/config.org" "~/Emacs/calendar-beorg.org")
 org-capture-templates '(("t" "Todo" entry
			  (file+olp+datetree "~/Dropbox/Emacs/Todo.org")
			  "* TODO %^{Headline}\n%?" :clock-in nil :clock-resume nil)
			 ("0" "Quick Capture - Todo" entry
			  (file+olp+datetree "~/Dropbox/Emacs/Todo.org")
			  "* TODO %^{Headline}" :clock-in nil :clock-resume nil
			  :immediate-finish 1)
			 ("l" "Log (Clocks In)" entry
			  (file+olp+datetree "~/Dropbox/Emacs/Todo.org")
			  "* %^{Headline}\n%?" :clock-in t :clock-resume t)
			 ("p" "Project" entry
			  (file+headline "~/Dropbox/Emacs/Todo.org" "PROJECTS")
			  "* PROJECT %^{Headline}\n%?" :clock-in nil :clock-resume nil)
			 ("n" "Note" entry
			  (file+headline "~/Dropbox/Emacs/Notes.org"
			   "NOTES TO PROCESS")
			  "* %^{Headline}\n%?" :clock-in nil :clock-resume nil)
			 ("j" "Journal" entry
			  (file+olp+datetree "~/Dropbox/Emacs/Journal.org")
			  "* %^{Headline}\n%?" :clock-in nil :clock-resume nil)
			 )
 org-persist-after-read-hook '(org-element--cache-persist-after-read)
 org-refile-targets '((org-agenda-files :maxlevel . 9))
 org-export-before-parsing-hook '(org-attach-expand-links)
 org-cycle-tab-first-hook '(org-babel-hide-result-toggle-maybe
			    org-babel-header-arg-expand)
 org-download-method 'attach
 org-archive-hook '(org-attach-archive-delete-maybe)
 org-speed-commands '(("a" . org-attach-reveal-in-emacs)
		      ("A" . org-archive-subtree-default-with-confirmation)
		      ("&" . org-mark-ring-goto) ("o" . jqg/speed-link-o)
		      ("z" . org-add-note) ("Outline Navigation")
		      ("n" org-speed-move-safe 'org-next-visible-heading)
		      ("p" org-speed-move-safe 'org-previous-visible-heading)
		      ("f" org-speed-move-safe 'org-forward-heading-same-level)
		      ("b" org-speed-move-safe 'org-backward-heading-same-level)
		      ("F" . org-next-block) ("B" . org-previous-block)
		      ("u" org-speed-move-safe 'outline-up-heading) ("j" . org-goto)
		      ("g" org-refile '(4)) ("Outline Visibility") ("c" . org-cycle)
		      ("C" . org-shifttab) (" " . org-display-outline-path)
		      ("s" . org-toggle-narrow-to-subtree) ("k" . org-cut-subtree)
		      ("=" . org-columns) ("Outline Structure Editing")
		      ("U" . org-metaup) ("D" . org-metadown) ("r" . org-metaright)
		      ("l" . org-metaleft) ("R" . org-shiftmetaright)
		      ("L" . org-shiftmetaleft)
		      ("i" progn (forward-char 1)
		       (call-interactively 'org-insert-heading-respect-content))
		      ("^" . org-sort) ("w" . org-refile)
		      ("a" . org-archive-subtree-default-with-confirmation)
		      ("@" . org-mark-subtree) ("#" . org-toggle-comment)
		      ("Clock Commands") ("I" . org-clock-in) ("O" . org-clock-out)
		      ("Meta Data Editing") ("t" . org-todo) ("," org-priority)
		      ("0" org-priority 32) ("1" org-priority 65)
		      ("2" org-priority 66) ("3" org-priority 67)
		      (":" . org-set-tags-command) ("e" . org-set-effort)
		      ("E" . org-inc-effort)
		      ("W" lambda (m) (interactive "sMinutes before warning: ")
		       (org-entry-put (point) "APPT_WARNTIME" m))
		      ("Agenda Views etc") ("v" . org-agenda) ("/" . org-sparse-tree)
		      ("Misc") ("o" . org-open-at-point)
		      ("?" . org-speed-command-help)
		      ("<" org-agenda-set-restriction-lock 'subtree)
		      (">" org-agenda-remove-restriction-lock))
 org-file-apps '((auto-mode . emacs) (directory . emacs) ("\\.mm\\'" . default)
		 ("\\.x?html?\\'" . default) ("\\.pdf\\'" . default)
		 ("\\.m4a\\'" . default) ("\\.m4v\\'" . default)
		 ("\\.mp3\\'" . default) ("\\.wav\\'" . default)
		 ("\\.jpg\\'" . default) ("\\.jpeg\\'" . default)
		 ("\\.png\\'" . default) ("\\.tiff\\'" . default)
		 ("\\.docx\\'" . default))
 org-columns-default-format "%50ITEM(Task) %10CLOCKSUM %16TIMESTAMP_IA"
 org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-show-empty-lines
		  org-cycle-optimize-window-after-visibility-change
		  org-cycle-display-inline-images)
 org-persist-before-read-hook '(org-element--cache-persist-before-read)
 org-image-actual-width 400
 org-attach-use-inheritance nil
 org-mode-hook '((lambda nil (org-bullets-mode 1)) org-clock-load
		 #[0 "\300\301\302\303\304$\207"
		   [add-hook change-major-mode-hook org-fold-show-all append local] 5]
		 #[0 "\300\301\302\303\304$\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-follow-link-hook '(recenter-top-bottom)
 org-babel-load-languages '((shell . t))
 org-agenda-skip-deadline-if-done t
 org-id-ts-format "%Y%m%d%H%M%S"
 org-agenda-start-with-log-mode t
 org-agenda-time-grid '((daily today required-time) nil "......" "----------------")
 org-agenda-span 'day
 org-download-timestamp "%Y%m%d%H%M%S_"
 org-download-abbreviate-filename-function 'expand-file-name
 org-present-mode-hook '((lambda nil (olivetti-set-width 20) (hide-mode-line-mode 1)
			  (org-present-big) (org-display-inline-images))
			 )
 org-present-mode-quit-hook '((lambda nil (olivetti-set-width 79)
			       (hide-mode-line-mode 0) (org-present-small))
			      )
 org-download-annotate-function 'dummy-org-download-annotate-function
 outline-isearch-open-invisible-function 'outline-isearch-open-invisible
 org-agenda-sorting-strategy '((agenda scheduled-up time-up deadline-up)
			       (todo alpha-up) (tags alpha-up)
			       (search category-up tag-up))
 org-startup-indented t
 org-fold-catch-invisible-edits 'error
 org-use-speed-commands t
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-agenda-after-show-hook '((lambda nil (org-narrow-to-subtree)
			       (org-fold-show-children))
			      )
 org-complete-tags-always-offer-all-agenda-tags t
 org-src-mode-hook '(org-src-babel-configure-edit-buffer
		     org-src-mode-configure-edit-buffer)
 org-agenda-window-setup 'current-window
 org-cycle-separator-lines 0
 org-todo-keywords '((sequence "TODO(t)" "PROJECT(p)" "NEXT(n)" "WAITING(w)" "|"
		      "DONE" "CANCELLED")
		     )
 org-id-link-to-org-use-id 'create-if-interactive
 org-structure-template-alist '(("a" . "export ascii") ("c" . "center")
				("C" . "comment") ("e" . "example") ("E" . "export")
				("h" . "export html") ("l" . "export latex")
				("q" . "quote") ("s" . "src") ("v" . "verse")
				("sl" . "src emacs-lisp"))
 org-blocker-hook '(org-block-todo-from-children-or-siblings-or-parent)
 org-speed-command-hook '(org-speed-command-activate org-babel-speed-command-activate)
 org-enforce-todo-dependencies t
 org-bullets-bullet-list '("►")
 org-todo-repeat-hook '(org-reset-checkbox-state-subtree)
 org-confirm-babel-evaluate nil
 org-fold-core-isearch-open-function 'org-fold--isearch-reveal
 org-clock-persist t
 org-persist-before-write-hook '(org-element--cache-persist-before-write)
 org-tab-first-hook '(org-babel-hide-result-toggle-maybe org-babel-header-arg-expand)
 org-link-shell-confirm-function nil
 org-babel-pre-tangle-hook '(save-buffer)
 org-agenda-loop-over-headlines-in-active-region nil
 org-fontify-quote-and-verse-blocks t
 org-agenda-start-on-weekday t
 org-attach-id-dir "~/Emacs/Files"
 org-attach-method 'mv
 org-occur-hook '(org-first-headline-recenter)
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-link-parameters '(("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 :insert-description
			org-info-description-as-command)
		       ("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)
		       ("attachment" :follow org-attach-follow :complete
			org-attach-complete-link)
		       ("id" :follow org-id-open) ("file+sys") ("file+emacs")
		       ("shell" :follow org-link--open-shell)
		       ("news" :follow
			#[514 "\301\300\302\x04Q\x02\"\207" ["news" browse-url ":"] 6
			  "\n\n(fn URL ARG)"]
			)
		       ("mailto" :follow
			#[514 "\301\300\302\x04Q\x02\"\207" ["mailto" browse-url ":"] 6
			  "\n\n(fn URL ARG)"]
			)
		       ("https" :follow
			#[514 "\301\300\302\x04Q\x02\"\207" ["https" browse-url ":"] 6
			  "\n\n(fn URL ARG)"]
			)
		       ("http" :follow
			#[514 "\301\300\302\x04Q\x02\"\207" ["http" browse-url ":"] 6
			  "\n\n(fn URL ARG)"]
			)
		       ("ftp" :follow
			#[514 "\301\300\302\x04Q\x02\"\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-metaup-hook '(org-babel-load-in-session-maybe)
 org-agenda-remove-tags t
 org-download-heading-lvl nil
 org-startup-with-inline-images t
 org-blank-before-new-entry '((heading) (plain-list-item))
 org-download-link-format-function 'jqg/org-download-link-format-function-default
 org-agenda-dim-blocked-tasks nil
 org-link-frame-setup '((vm . vm-visit-folder-other-frame)
			(vm-imap . vm-visit-imap-folder-other-frame)
			(gnus . org-gnus-no-new-news) (file . find-file)
			(wl . wl-other-frame) (dir . dired-other-window))
 org-return-follows-link t
 org-tags-column 0
 org-id-method 'ts
 org-clock-history-length 35
 org-download-image-dir "~/Emacs/Files/"
 org-attach-store-link-p 'file
 org-footnote-section nil
 )


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