Bug: org-adapt-indentation is not compatible with paragraph-indent-minor-mode [9.4.5 (9.4.5-16-g94be20-elpaplus @ /home/lockywolf/.emacs.d/elpa/org-plus-contrib-20210412/)]

[Vladimir Nikishkin <lockywolf@gmail.com>]

Hello, everyone.

Basically, my bug report is roughly about the subject.
`paragraph-indent-minor-mode` is shipped with Emacs by default (just like
org), and its behaviour is very standard for a lot of languages. A one
or two spaces indentation starts a new paragraph in quite a few human
languages.

However, turning on `paragraph-indent-minor-mode` seemingly disables
org's automatic indentation to the first letter of a heading, regardless
of `org-adapt-indentation` being set.

I think that with paragraph-indent-minor-mode, paragraphs should start
by adding "two more spaces" to the indentation, like this:

#+begin_example
* Heading one
  First paragraph is a paragraph even if not indented.
    Second paragraph is a paragraph because indented.
  This line belongs to the second paragraph.

  Third paragraph is a paragraph even if not indented because of a
  newline.

    But fourth paragraph can be indented too. And the very long line I
  have written should be wrapped like this.

** Heading two
     This is also a start of a paragraph.
     This line starts a new paragraph too.
   Normal level-two indentation.
#+end_example

It would be nice if the two modes shipped with emacs were compatible, at
least to a degree at which indentation works.

Emacs  : GNU Emacs 27.1 (build 1, x86_64-slackware-linux-gnu, GTK+ Version 3.24.24)
 of 2021-02-18
Package: Org mode version 9.4.5 (9.4.5-16-g94be20-elpaplus @ /home/lockywolf/.emacs.d/elpa/org-plus-contrib-20210412/)

current state:
==============
(setq
 org-icalendar-store-UID t
 org-src-mode-hook '(#2=
                     (closure #1=
                      ((--cl-my-org-confirm-babel-evaluate-- closure #1# (lang body)
                        "Define by lockywolf to silence org-babel.\nLANG is what is after begin_src, and BODY is ignored"
                        (not
                         (or (string= lang "plantuml") (string= lang "C") (string= lang "scheme") (string= lang "fortran")
                          (string= lang "f90") (string= lang "elisp") (string= lang "latex") (string= lang "shell"))
                         )
                        )
                       (--cl-syntax-improver-- . #2#) t)
                      nil
                      (progn (message "Improving syntax for org-mode.") (modify-syntax-entry 60 ".") (modify-syntax-entry 62 ".")
                       (setq geiser-autodoc--inhibit t))
                      )
                     org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer)
 org-agenda-scheduled-leaders '("Scheduled: " "Sched.%4dx: ")
 org-after-todo-state-change-hook '(org-checklist)
 org-latex-listings t
 org-link-shell-confirm-function 'yes-or-no-p
 org-babel-after-execute-hook '(org-redisplay-inline-images)
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-export-with-sub-superscripts '{}
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 org-html-format-inlinetask-function 'org-html-format-inlinetask-default-function
 org-icalendar-combined-agenda-file "~/Personal_Planner/Journal/org-journal-export.ics"
 org-pretty-entities t
 org-special-ctrl-k t
 org-odt-format-headline-function 'org-odt-format-headline-default-function
 org-special-ctrl-a/e t
 org-latex-pdf-process '("latexmk -e '$biber=qq(biber --isbn-normalise)' -lualatex -outdir=%o -f %f")
 org-agenda-files '("~/Personal_Planner/Planner.org" "~/Personal_Planner/notes.org"
                    "~/Personal_Planner/2020-04-28-hotkeys-to-remember.txt.org" "/home/lockywolf/Personal_Planner/Journal/20210701")
 org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default
 org-reveal-start-hook '(org-decrypt-entry)
 org-modules '(org-habit ol-w3m ol-bbdb ol-bibtex ol-docview ol-gnus ol-info ol-irc ol-mhe ol-rmail ol-eww)
 org-plantuml-jar-path "/usr/local/bin/plantuml.jar"
 org-startup-folded t
 org-mode-hook '((closure #1=
                  ((--cl-my-org-confirm-babel-evaluate-- closure #1# (lang body)
                    "Define by lockywolf to silence org-babel.\nLANG is what is after begin_src, and BODY is ignored"
                    (not
                     (or (string= lang "plantuml") (string= lang "C") (string= lang "scheme") (string= lang "fortran")
                      (string= lang "f90") (string= lang "elisp") (string= lang "latex") (string= lang "shell"))
                     )
                    )
                   (--cl-syntax-improver-- . #2=
                    (closure #1# nil
                     (progn (message "Improving syntax for org-mode.") (modify-syntax-entry 60 ".") (modify-syntax-entry 62 ".")
                      (setq geiser-autodoc--inhibit t))
                     )
                    )
                   t)
                  nil (setq reftex-cite-format '((111 . "cite:%l") (104 . "\\cite{%l}"))))
                 turn-on-org-cdlatex #2# org-clock-load org-tempo-setup org-fancy-priorities-mode
                 #[0 "\300\301\302\303\304$\207" [add-hook change-major-mode-hook org-show-all append local] 5]
                 #[0 "\300\301\302\303\304$\207" [add-hook change-major-mode-hook org-babel-show-result-all append local] 5]
                 org-babel-result-hide-spec org-babel-hide-all-hashes
                 #[0 "\301\211.\207" [imenu-create-index-function org-imenu-get-tree] 2] org-eldoc-load)
 org-clock-persist 'history
 org-fancy-priorities-list '((65 . "❗") (66 . "⬆") (67 . "⬇") (68 . "☕") (49 . "⚡") (50 . "⮬") (51 . "⮮") (52 . "☕")
                             (73 . "Important"))
 org-yank-adjusted-subtrees t
 org-export-with-smart-quotes t
 org-odt-format-drawer-function #[514 "\207" [] 3 "\n\n(fn NAME CONTENTS)"]
 org-archive-hook '(org-attach-archive-delete-maybe)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-agenda-finalize-hook '(org-fancy-priorities-create-overlays)
 org-journal-mode-hook '(#[0 "\301\b\302\303\304$\207" [org-journal-encrypt-on add-hook org-journal-encryption-hook nil t] 5]
                         (lambda nil (add-hook org-journal-encrypt-on 'org-journal-encryption-hook nil t)))
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-preview-latex-default-process 'imagemagick
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-bibtex-headline-format-function #[257 "\300.\236A\207" [:title] 3 "\n\n(fn ENTRY)"]
 org-latex-format-drawer-function #[514 "\207" [] 3 "\n\n(fn _ CONTENTS)"]
 org-babel-pre-tangle-hook '(save-buffer)
 org-latex-compiler "lualatex"
 org-tab-first-hook '(org-babel-hide-result-toggle-maybe org-babel-header-arg-expand)
 org-babel-load-languages '((plantuml . t) (C . t) (scheme . t) (latex . t) (shell . t) (fortran . t))
 org-log-done 'time
 org-journal-date-format "%F %A, %d %B %Y"
 org-load-hook '(org-pdftools-setup-link)
 org-sidebar-window-after-display-hook '((lambda nil "Set window-parameter `mode-line-format' to nil."
                                          (set-window-parameter nil 'mode-line-format 'none))
                                         )
 org-checklist-export-function 'org-export-as-ascii
 org-startup-align-all-tables t
 org-ascii-format-drawer-function #[771 ".\207" [] 4 "\n\n(fn NAME CONTENTS WIDTH)"]
 org-ellipsis "↴"
 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-icalendar-include-todo "all"
 org-mru-clock-completing-read 'ido-completing-read
 org-catch-invisible-edits 'show
 org-occur-hook '(org-first-headline-recenter)
 org-log-into-drawer t
 org-edit-src-auto-save-idle-delay 15
 org-journal-prefix-key "C-c j "
 org-agenda-include-diary t
 org-journal-enable-agenda-integration t
 org-structure-template-alist '(("bash" . "src shell :exports both :results output :eval no")
                                ("F" . "src f90 :exports both :results output") ("EL" . "src elisp :exports both :results output")
                                ("SE" . "src scheme :exports code :wrap example") ("SV" . "src scheme :exports both :results value")
                                ("SO" . "src scheme :exports both :results output")
                                ("p" . "src plantuml :noweb no :exports both :file ") ("a" . "export ascii") ("c" . "center")
                                ("C" . "comment") ("e" . "example") ("E" . "export") ("h" . "export html") ("l" . "export latex")
                                ("q" . "quote") ("s" . "src") ("v" . "verse"))
 org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-show-empty-lines
                  org-optimize-window-after-visibility-change)
 org-edit-src-turn-on-auto-save t
 org-todo-keywords '((sequence "TODO" "|" "DONE") (sequence "|" "CANCELLED"))
 org-speed-command-hook '(org-speed-command-activate org-babel-speed-command-activate)
 org-hierarchical-todo-statistics nil
 org-preview-latex-process-alist '((dvipng :programs ("latex" "dvipng") :description "dvi > png" :message
                                    "you need to install the programs: latex and dvipng." :image-input-type "dvi" :image-output-type
                                    "png" :image-size-adjust (1.0 . 1.0) :latex-compiler
                                    ("latex -interaction nonstopmode -output-directory %o %f") :image-converter
                                    ("dvipng -D %D -T tight -o %O %f"))
                                   (dvisvgm :programs ("latex" "dvisvgm") :description "dvi > svg" :message
                                    "you need to install the programs: latex and dvisvgm." :image-input-type "dvi"
                                    :image-output-type "svg" :image-size-adjust (1.7 . 1.5) :latex-compiler
                                    ("latex -interaction nonstopmode -output-directory %o %f") :image-converter
                                    ("dvisvgm %f -n -b min -c %S -o %O"))
                                   (imagemagick :programs ("latex" "convert") :description "pdf > png" :message
                                    "you need to install the programs: latex and imagemagick." :image-input-type "pdf"
                                    :image-output-type "png" :image-size-adjust (1.0 . 1.0) :latex-compiler
                                    ("lualatex -interaction nonstopmode -output-directory %o %f") :image-converter
                                    ("convert -density %D -trim -antialias %f -quality 100 %O"))
                                   )
 org-odt-format-inlinetask-function 'org-odt-format-inlinetask-default-function
 org-mru-clock-format-function 'substring-no-properties
 org-clock-auto-clockout-timer 300
 org-journal-dir "~/Personal_Planner/Journal/"
 org-babel-tangle-lang-exts '(("fortran" . "F90") ("latex" . "tex") ("D" . "d") ("C++" . "cpp") ("emacs-lisp" . "el")
                              ("elisp" . "el"))
 org-format-latex-options '(:foreground default :background default :scale 3.0 :html-foreground "Black" :html-background
                            "Transparent" :html-scale 1.0 :matchers ("begin" "$1" "$" "$$" "\\(" "\\["))
 org-refile-use-outline-path 'full-file-path
 org-clock-in-hook '(org-clock-auto-clockout)
 org-export-before-parsing-hook '(org-attach-expand-links)
 org-latex-listings-langs '((f90 "Fortran") (patch "bash") (shell "bash") (plantuml "MetaPost") (elisp "elisp") (scheme "Lisp")
                            (emacs-lisp "Lisp") (lisp "Lisp") (clojure "Lisp") (c "C") (cc "C++") (fortran "fortran") (perl "Perl")
                            (cperl "Perl") (python "Python") (ruby "Ruby") (html "HTML") (xml "XML") (tex "TeX")
                            (latex "[LaTeX]TeX") (shell-script "bash") (gnuplot "Gnuplot") (ocaml "[Objective]Caml") (caml "Caml")
                            (sql "SQL") (sqlite "sql") (makefile "make") (R "r"))
 org-confirm-shell-link-function 'yes-or-no-p
 org-link-parameters '(("attachment" :follow org-attach-follow :complete org-attach-complete-link) ("id" :follow org-id-open)
                       ("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)
                       ("mairix" :follow org-mairix-open :store org-mairix-store-gnus-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)
                       ("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)
                       ("org-ql-search" :follow org-ql-view--link-follow :store org-ql-view--link-store)
                       ("yt" :follow (closure #1=(t) (handle) (browse-url (concat "https://www.youtube.com/embed/" handle))) :export
                        (closure #1# (path desc backend)
                         (cond ((eql backend 'html) (format yt-iframe-format path (or desc "")))
                          ((eql backend 'latex) (format "href{%s}{%s}" path (or desc "video"))))
                         )
                        )
                       ("ebib" :follow org-ebib-open :store org-ebib-store-link)
                       ("bibtex" :follow org-bibtex-open :store org-bibtex-store-link) ("cite" :follow org-ebib-open :export nil)
                       ("mu4e" :follow mu4e-org-open :store mu4e-org-store-link)
                       ("elfeed" :follow elfeed-link-open :store elfeed-link-store-link) ("file+sys") ("file+emacs")
                       ("shell" :follow org-link--open-shell)
                       (#2="news" :follow #[514 #3="\301\300\302.Q.\"\207" [#2# browse-url #5=":"] 6 #6="\n\n(fn URL ARG)"])
                       (#4="mailto" :follow #[514 #3# [#4# browse-url #5#] 6 #6#])
                       (#7="https" :follow #[514 #3# [#7# browse-url #5#] 6 #6#])
                       (#8="http" :follow #[514 #3# [#8# browse-url #5#] 6 #6#])
                       (#9="ftp" :follow #[514 #3# [#9# browse-url #5#] 6 #6#]) ("help" :follow org-link--open-help)
                       ("file" :complete org-link-complete-file) ("elisp" :follow org-link--open-elisp)
                       ("doi" :follow org-link--open-doi))
 org-journal-file-type 'monthly
 org-latex-format-headline-function 'org-latex-format-headline-default-function
 org-agenda-start-with-follow-mode t
 org-capture-templates '(("t" "Todo" entry (file+headline "~/Personal_Planner/Planner.org" "Incoming stuff") "* TODO %?\n  %i\n  %a")
                         ("j" "Journal entry" plain #'#1=
                          (closure ((--cl-org-journal-find-location-- . #1#) t) nil
                           (progn (org-journal-new-entry t) (if (eq org-journal-file-type 'daily) nil (org-narrow-to-subtree))
                            (goto-char (point-max)))
                           )
                          "** %(format-time-string org-journal-time-format)%^{Title}\n%i%?" :jump-to-captured t :immediate-finish t)
                         )
 org-link-elisp-confirm-function 'yes-or-no-p
 org-journal-time-format "%T %Z(%:::z)"
 org-latex-format-inlinetask-function 'org-latex-format-inlinetask-default-function
 org-tab-before-tab-emulation-hook '(org-tempo-complete-tag)
 org-html-format-drawer-function #[514 "\207" [] 3 "\n\n(fn NAME CONTENTS)"]
 org-latex-packages-alist '((#1="" "color") (#1# "listings"))
 org-image-actual-width nil
 org-extend-today-until 3
 org-use-tag-inheritance nil
 org-html-use-infojs nil
 org-latex-classes '(("beamer" "\\documentclass[presentation]{beamer}" ("\\section{%s}" . "\\section*{%s}")
                      ("\\subsection{%s}" . "\\subsection*{%s}") ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
                     ("acmart" "\\documentclass[sigplan,nonacm,natbib=false]{acmart}" ("\\section{%s}" . "\\section*{%s}")
                      ("\\subsection{%s}" . "\\subsection*{%s}") ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
                     ("article" "\\documentclass[11pt]{article}" ("\\section{%s}" . "\\section*{%s}")
                      ("\\subsection{%s}" . "\\subsection*{%s}") ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
                      ("\\paragraph{%s}" . "\\paragraph*{%s}") ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
                     ("report" "\\documentclass[11pt]{report}" ("\\part{%s}" . "\\part*{%s}") ("\\chapter{%s}" . "\\chapter*{%s}")
                      ("\\section{%s}" . "\\section*{%s}") ("\\subsection{%s}" . "\\subsection*{%s}")
                      ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
                     ("book" "\\documentclass[11pt]{book}" ("\\part{%s}" . "\\part*{%s}") ("\\chapter{%s}" . "\\chapter*{%s}")
                      ("\\section{%s}" . "\\section*{%s}") ("\\subsection{%s}" . "\\subsection*{%s}")
                      ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
                     )
 org-html-format-headline-function 'org-html-format-headline-default-function
 org-mairix-display-hook 'org-mairix-gnus-display-results
 org-confirm-babel-evaluate '#1=(closure #2=
                                 ((--cl-my-org-confirm-babel-evaluate-- . #1#)
                                  (--cl-syntax-improver-- closure #2# nil
                                   (progn (message "Improving syntax for org-mode.") (modify-syntax-entry 60 ".")
                                    (modify-syntax-entry 62 ".") (setq geiser-autodoc--inhibit t))
                                   )
                                  t)
                                 (lang body)
                                 "Define by lockywolf to silence org-babel.\nLANG is what is after begin_src, and BODY is ignored"
                                 (not
                                  (or (string= lang "plantuml") (string= lang "C") (string= lang "scheme") (string= lang "fortran")
                                   (string= lang "f90") (string= lang "elisp") (string= lang "latex") (string= lang "shell"))
                                  )
                                 )
 org-use-sub-superscripts '{}
 org-agenda-custom-commands '(("n" "Agenda and all TODO" ((agenda #1="" nil) (alltodo #1# nil)) nil
                               "/run/user/1000/agenda-snapshot.txt")
                              )
 org-link-from-user-regexp "\\<lockywolf@laptop\\.lockywolf\\.net\\>\\|\\<Vladimir Nikishkin\\>"
 org-latex-listings-options '(("numbers" "none") ("frame" "single") ("basicstyle" "\\footnotesize\\ttfamily ")
                              ("keywordstyle" "\\ttfamily") ("upquote" "true") ("extendedchars" "true"))
 org-use-speed-commands t
 org-ql-sidebar-buffer-setup-hook '(toggle-truncate-lines)
 org-mairix-gnus-select-display-group-function 'org-mairix-gnus-select-display-group-function-gg
 org-latex-bib-compiler "biber"
 org-default-notes-file "~/Personal_Planner/notes.org"
 )
-- 
Your sincerely,
Vladimir Nikishkin (MiEr, lockywolf)
(Laptop)