[BUG] org-babel-execute-subtree removes all overlays (org-fold-save-outline-visibility) [9.7-pre, gfb61e8]

[Bruno Barbier <brubar.cs@gmail.com>]

Hi,

Org removes all overlays when calling org-babel-execute-subtree.

Here is a way to reproduce:

    #+begin_src elisp
      (with-temp-buffer
        (let (ovl
              (statuses nil)
              (live-p (lambda (xo) (or (and (overlay-buffer xo) "alive") "dead")))) 
          (insert "* Mandatory heading")
          (org-mode)
          (setq ovl (make-overlay (point-min) (point-max)))
          (push (list "before"  (funcall live-p ovl))  statuses)
          (org-babel-execute-subtree)
          (push (list "after"  (funcall live-p ovl)) statuses)
          (nreverse statuses)))
    #+end_src

    #+RESULTS:
    | before | alive |
    | after  | dead  |

Org should not remove overlays it doesn't own.

After investigation, it seems that any use of
`org-save-outline-visibility' will call:

    (org-fold-core-region START END nil)
                                    ^^^

which will, indeed, remove any overlay (except for those that are
both 'org-invisible and 'invisible).

Thanks,

Bruno


Emacs  : GNU Emacs 30.0.50 (build 1, x86_64-pc-linux-gnu, X toolkit, cairo version 1.18.0)
 of 2024-03-12
Package: Org mode version 9.7-pre (release_9.6.20-1281-gfb61e8.dirty @ /home/bruno/work/open-src/emacs/orgmode/orgmode/lisp/)

current state:
==============
(setq
 org-yank-image-file-name-function 'org-yank-image-autogen-filename
 org-persist-before-write-hook '(org-element--cache-persist-before-write)
 org-html-format-headline-function 'org-html-format-headline-default-function
 org-html-format-drawer-function #[514 "\207" [] 3 ("/home/bruno/work/open-src/emacs/orgmode/orgmode/lisp/ox-html.elc" . 24162)]
 org-latex-format-inlinetask-function 'org-latex-format-inlinetask-default-function
 org-speed-command-hook '(org-speed-command-activate org-babel-speed-command-activate)
 org-persist-after-read-hook '(org-element--cache-persist-after-read)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-latex-format-headline-function 'org-latex-format-headline-default-function
 org-latex-format-drawer-function #[514 "\207" [] 3 ("/home/bruno/work/open-src/emacs/orgmode/orgmode/lisp/ox-latex.elc" . 37582)]
 org-mode-hook '(#[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-confirm-shell-link-function 'yes-or-no-p
 org-odt-format-headline-function 'org-odt-format-headline-default-function
 org-archive-hook '(org-attach-archive-delete-maybe)
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-occur-hook '(org-first-headline-recenter)
 org-html-format-inlinetask-function 'org-html-format-inlinetask-default-function
 org-ascii-format-drawer-function #[NON PRINTABLE]
 org-bibtex-headline-format-function 'org-bibtex-headline-format-default
 org-link-parameters '(("attachment" :follow org-attach-follow :complete org-attach-complete-link)
		       ("id" :follow org-id-open :store org-id-store-link-maybe)
		       ("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)
		       ("file+sys") ("file+emacs") ("shell" :follow org-link--open-shell)
		       ("news" :follow
			#[ ---NON PRINTABLE--- ]
			  ("/home/bruno/work/open-src/emacs/orgmode/orgmode/lisp/ol.elc" . 52731)]
			)
		       ("mailto" :follow
			#[ ---NON PRINTABLE--- ]
			)
		       ("https" :follow
			#[ ---NON PRINTABLE--- ]
			)
		       ("http" :follow
			#[ ---NON PRINTABLE--- ]
			)
		       ("ftp" :follow
			#[ ---NON PRINTABLE--- ]
			)
		       ("help" :follow org-link--open-help :store org-link--store-help) ("file" :complete org-link-complete-file)
		       ("elisp" :follow org-link--open-elisp))
 org-persist-directory "/tmp/org-persist-6fkhMh"
 org-cycle-tab-first-hook '(org-babel-hide-result-toggle-maybe org-babel-header-arg-expand)
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-tab-first-hook '(org-babel-hide-result-toggle-maybe org-babel-header-arg-expand)
 org--warnings nil
 org-babel-pre-tangle-hook '(save-buffer)
 org-export-before-parsing-hook '(org-attach-expand-links)
 org-link-shell-confirm-function 'yes-or-no-p
 org-fold-core-isearch-open-function 'org-fold--isearch-reveal
 outline-isearch-open-invisible-function 'outline-isearch-open-invisible
 org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer)
 org-agenda-loop-over-headlines-in-active-region nil
 org-link-elisp-confirm-function 'yes-or-no-p
 org-odt-format-inlinetask-function 'org-odt-format-inlinetask-default-function
 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-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default
 org-odt-format-drawer-function #[514 "\207" [] 3 ("/home/bruno/work/open-src/emacs/orgmode/orgmode/lisp/ox-odt.elc" . 18494)]
 )