bug#58479: 29.0.50; [feature/noverlay] Displaced overlays in notmuch search buffers after refreshing

[Ihor Radchenko <yantar92@gmail.com>]

Hi,

As I mentioned in
https://yhetil.org/emacs-devel/jwvo7ulzmvv.fsf-monnier+emacs@gnu.org/, I
consistently observe issues with overlays in notmuch search buffers on
feature/noverlay branch.

I have tested with Emacs 29 master vs. feature/noverlay and confirm that
the problem only appears in feature/noverlays.

I do not have a good recipe starting from emacs -Q (not sure how to make
that for notmuch), but I will try to provide as much information as I
can.

When I do
1. M-x notmuch-search <RET> date:today <RET>
   notmuch search buffer with today's email is displayed on my system
   This search buffer uses overlays to truncate thread author list:

   Text content at position 35:


There is an overlay here:
 From 35 to 68
  invisible            ellipsis
  isearch-open-invisible delete-overlay


There are text properties here:
  face                 (notmuch-search-flagged-face notmuch-search-non-matching-authors)
  notmuch-search-result [Show]

 At this point, no anomaly is observed
2. I hit "r" to refresh current notmuch buffer
   Unexpectedly, "..." (depicting hidden overlays) appear at bob.
   M-x describe-text-properties on the strange overlay yields:

   There are 12 overlays here:
 From 1 to 1
  invisible            ellipsis
  isearch-open-invisible delete-overlay
 From 1 to 1
  invisible            ellipsis
  isearch-open-invisible delete-overlay
 ....

3. I hit "r" again and I get 24 overlays ther
4. The number of overlays grows proportionally with number of times I
   hit "r"

I tried to debug a bit further and noted that running
M-: (let ((inhibit-read-only t)) (erase-buffer))
in the search buffer followed by
M-: (overlays-in (point-min) (point-max))
yields non-nil -- overlays are not cleared upon deleting the containing text.

In GNU Emacs 29.0.50 (build 1, x86_64-pc-linux-gnu, GTK+ Version
 3.24.34, cairo version 1.16.0) of 2022-10-12 built on yantar92-laptop
Repository revision: 12836db6e4e09378d41301b3d4e1fcff58132d3a
Repository branch: feature/noverlay
Windowing system distributor 'The X.Org Foundation', version 11.0.12101004
System Description: Gentoo Linux

Configured features:
ACL CAIRO DBUS FREETYPE GIF GLIB GMP GNUTLS GPM GSETTINGS HARFBUZZ JPEG
JSON LCMS2 LIBXML2 MODULES NOTIFY INOTIFY PDUMPER PNG RSVG SECCOMP SOUND
SQLITE3 THREADS TIFF TOOLKIT_SCROLL_BARS WEBP X11 XDBE XIM XINPUT2 XPM
GTK3 ZLIB

Important settings:
  value of $LC_COLLATE: C
  value of $LANG: en_US.utf8
  locale-coding-system: utf-8-unix

Major mode: notmuch-search

Minor modes in effect:
  pyvenv-mode: t
  TeX-PDF-mode: t
  git-email-notmuch-mode: t
  git-email-piem-mode: t
  piem-notmuch-mode: t
  org-edna-mode: t
  eros-mode: t
  pdf-occur-global-minor-mode: t
  which-key-mode: t
  diredfl-global-mode: t
  winner-mode: t
  eval-sexp-fu-flash-mode: t
  global-flycheck-mode: t
  flycheck-mode: t
  el-patch-use-package-mode: t
  global-git-commit-mode: t
  magit-auto-revert-mode: t
  recentf-mode: t
  persistent-scratch-autosave-mode: t
  savehist-mode: t
  helm-adaptive-mode: t
  helm-mode: t
  helm-minibuffer-history-mode: t
  helm-ff-icon-mode: t
  shell-dirtrack-mode: t
  helm--remap-mouse-mode: t
  async-bytecomp-package-mode: t
  boon-mode: t
  boon-local-mode: t
  global-page-break-lines-mode: t
  shackle-mode: t
  override-global-mode: t
  straight-use-package-mode: t
  straight-package-neutering-mode: t
  global-eldoc-mode: t
  show-paren-mode: t
  electric-indent-mode: t
  mouse-wheel-mode: t
  global-prettify-symbols-mode: t
  file-name-shadow-mode: t
  global-font-lock-mode: t
  font-lock-mode: t
  window-divider-mode: t
  buffer-read-only: t
  line-number-mode: t
  indent-tabs-mode: t
  transient-mark-mode: t
  auto-composition-mode: t
  auto-encryption-mode: t
  auto-compression-mode: t
  abbrev-mode: t

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Features:
(shadow footnote emacsbug highlight-indentation elpy elpy-rpc pyvenv
eshell esh-cmd esh-ext esh-opt esh-proc esh-io esh-arg esh-module
esh-groups esh-util elpy-shell elpy-profile elpy-django elpy-refactor
grep descr-text helm-command helm-elisp helm-eval font-latex latex
latex-flymake flymake-proc flymake tex-ispell tex-style tex tex-mode
org-duration cal-iso vc org-table-sticky-header oc-basic ffap
tramp-archive tramp-gvfs helm-x-files helm-for-files helm-bookmark
helm-external helm-net git-email-magit magit-patch git-email-notmuch
git-email-piem git-email git-email-autoloads project-autoloads
xref-autoloads piem-notmuch piem piem-maildir mail-extr piem-autoloads
org-crypt helm-notmuch helm-notmuch-autoloads ol-notmuch
ol-notmuch-autoloads org-eldoc org-table-sticky-header-autoloads
posframe posframe-autoloads ob-async ob-async-autoloads ob-latex ob-dot
ob-calc calc-store calc-trail ob-gnuplot ob-ditaa ob-C cc-mode cc-fonts
cc-guess cc-menus cc-cmds cc-styles cc-align cc-engine cc-vars cc-defs
ob-python ob-perl ob-org ob-shell ob-mathematica
ob-mathematica-autoloads org-tempo tempo org-archive ox-md ox-beamer
engrave-faces engrave-faces-autoloads ox-extra orgdiff orgdiff-autoloads
doct ya-org-capture ya-org-capture-autoloads doct-autoloads
org-capture-pop-frame org-capture-pop-frame-autoloads org-protocol
org-analyzer-autoloads pomidor-autoloads alert-autoloads log4e-autoloads
gntp-autoloads helm-org-ql helm-org org-clock org-autosort
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org-contacts gnus-art mm-uu mml2015 gnus-sum gnus-group gnus-undo
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mm-decode mm-bodies mm-encode mail-parse rfc2231 rfc2047 rfc2045 mm-util
ietf-drums mail-prsvr mailabbrev mail-utils gmm-utils mailheader
pcvs-util add-log magit-core magit-autorevert magit-margin
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with-editor-autoloads transient-autoloads autorevert recentf tree-widget
disp-table hl-todo pretty-symbols company-oddmuse company-keywords
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shell parse-time iso8601 ls-lisp helm-buffers helm-occur helm-tags
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asoc asoc.el-autoloads no-littering compat no-littering-autoloads
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autoload loaddefs-gen generate-lisp-file radix-tree lisp-mnt easy-mmode
cl-seq pcase subr-x byte-opt cl-macs gv cl-loaddefs cl-lib bytecomp
byte-compile cconv server rmc iso-transl tooltip eldoc paren electric
uniquify ediff-hook vc-hooks lisp-float-type elisp-mode mwheel
term/x-win x-win term/common-win x-dnd tool-bar dnd fontset image
regexp-opt fringe tabulated-list replace newcomment text-mode lisp-mode
prog-mode register page tab-bar menu-bar rfn-eshadow isearch easymenu
timer select scroll-bar mouse jit-lock font-lock syntax font-core
term/tty-colors frame minibuffer nadvice seq simple cl-generic
indonesian philippine cham georgian utf-8-lang misc-lang vietnamese
tibetan thai tai-viet lao korean japanese eucjp-ms cp51932 hebrew greek
romanian slovak czech european ethiopic indian cyrillic chinese
composite emoji-zwj charscript charprop case-table epa-hook
jka-cmpr-hook help abbrev obarray oclosure cl-preloaded button loaddefs
faces cus-face macroexp files window text-properties overlay sha1 md5
base64 format env code-pages mule custom widget keymap
hashtable-print-readable backquote threads dbusbind inotify lcms2
dynamic-setting system-font-setting font-render-setting cairo
move-toolbar gtk x-toolkit xinput2 x multi-tty make-network-process
emacs)

Memory information:
((conses 16 12227780 1358744)
 (symbols 48 87874 1045)
 (strings 32 669678 172747)
 (string-bytes 1 20916974)
 (vectors 16 485755)
 (vector-slots 8 11739880 3327093)
 (floats 8 4841 5442)
 (intervals 56 237779 18133)
 (buffers 984 49))

-- 
Ihor Radchenko // yantar92,
Org mode contributor,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>