Cloned https://git.savannah.gnu.org/git/emacs/org-mode.git, changed to directory "org-mode", made "autoloads", started Emacs as "emacs -Q -L $PWD".
In an otherwise empty org-mode buffer, create a block #+begin_src shell # configure shell options and variables. bash-completion # requires shell option extglob, anyway, so set and use it # without further pondering about adverse consequences. shopt -s checkwinsize shopt -s direxpand shopt -s extglob #+end_src Move point into the comment part of that shell snippet and press M-q. The result should look like this: #+begin_src shell # configure shell options and variables. bash-completion requires # shell option extglob, anyway, so set and use it without further # pondering about adverse consequences. shopt -s checkwinsize shopt # -s direxpand shopt -s extglob #+end_src That is, code and comment got filled into one big comment. When changing into edit mode first, only the comment part gets filled, as it would happen also in a real sh-mode buffer. The root cause should be this snippet from `org-fill-element': (org-babel-do-in-edit-buffer ;; `org-babel-do-in-edit-buffer' will preserve region if it ;; is within src block contents. Otherwise, the region ;; crosses src block boundaries. We re-fill the whole src ;; block in such scenario. (when (and regionp (not (region-active-p))) (push-mark (point-min)) (goto-char (point-max)) (setq mark-active t)) (funcall-interactively #'fill-paragraph justify 'region)))) where `fill-paragraph' gets called with an active region. To me that seems strange, at least for source blocks. If this is really intended, it should probably be made configurable. Thanks Jens Emacs : GNU Emacs 28.2 (build 2, x86_64-pc-linux-gnu, X toolkit, cairo version 1.16.0, Xaw3d scroll bars) of 2023-03-14, modified by Debian Package: Org mode version 9.5.5 (release_9.5.5 @ /usr/share/emacs/28.2/lisp/org/) current state: ============== (setq org-link-elisp-confirm-function 'yes-or-no-p org-bibtex-headline-format-function #[257 "\300\236A\207" [:title] 3 "\n\n(fn ENTRY)"] org-export-before-parsing-hook '(org-attach-expand-links) org-archive-hook '(org-attach-archive-delete-maybe) org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-show-empty-lines org-optimize-window-after-visibility-change) org-mode-hook '(#[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-confirm-shell-link-function 'yes-or-no-p outline-isearch-open-invisible-function 'outline-isearch-open-invisible org-agenda-before-write-hook '(org-agenda-add-entry-text) org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer) org-confirm-elisp-link-function 'yes-or-no-p org-speed-command-hook '(org-speed-command-activate org-babel-speed-command-activate) org-tab-first-hook '(org-babel-hide-result-toggle-maybe org-babel-header-arg-expand) org-link-shell-confirm-function 'yes-or-no-p org-babel-pre-tangle-hook '(save-buffer) org-agenda-loop-over-headlines-in-active-region nil org-occur-hook '(org-first-headline-recenter) org-metadown-hook '(org-babel-pop-to-session-maybe) org-link-parameters '(("attachment" :follow org-attach-follow :complete org-attach-complete-link) ("id" :follow org-id-open) ("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) ("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-metaup-hook '(org-babel-load-in-session-maybe) )