Bug: clock-in from org-agenda freezes thread when enforce + todo keywords [9.4.4 (release_9.4.4 @ /usr/local/share/emacs/28.0.50/lisp/org/)]

[webdev@toryanderson.com (Tory S. Anderson)]

After long bisection and suffering for a while from this issue, I have narrowed down an issue that is breaking my workflow. I noticed that some time recently orgmode has begun freezing my system (as an exwm user, this is serious) when I attempt to clock in to certain tasks from the agenda. Clocking in from their actual orgmode file works just fine, but sometimes then even checking the agenda causes thread freezing (I see my CPU spike to maximum on that thread, and emacs becomes unresponsive). In my minimal reproducable version, no packages are loaded other than org-mode and use-package. Here is my current version, although I've been encountering this problem for longer than I've been using this version, probably.

Besides all the details included below by the bug report, Here is the use-package declaration that produces the frozen thread when you attempt to clock in to the "parent" item in your agenda (it may be important that the dates/deadlines are "today"; I don't know). In this toy example you can recover with C-g a time or two, but in my full setup even c-g can take up to 30 seconds to register.

Steps to reproduce:

1. load emacs with the use-package declaration below
2. visit =M-x org-agenda<RET>a3. Clock in to the "Parent" item on the agenda by highlighting it and doing =C-c C-x <TAB>   -- thread will freeze indefinitely, although in toy example you can break free with C-g

#+begin_src lisp
  (use-package org
      :straight (:type built-in)
      :demand t
      :custom
      (org-enforce-todo-dependencies t)

      (org-agenda-files
       '("~/org/nested.org"))

      (org-todo-keywords
       '((type "TODO(t)" "STARTED(s)" "UNSTARTED(u)" "|" "DONE(d)")
	 (type "PENDING(p)" "HOLD(h)" "ONGOING(o)" "|" "DONE(d)")
	 (sequence "|" "CANCELED(c)" "ABSTAINED(a)"))))
#+end_src

Here is nested.org : https://gitlab.com/-/snippets/2133558


------------------------------------------------------------------------
Emacs  : GNU Emacs 28.0.50 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.29, cairo version 1.16.0)
 of 2021-06-03
Package: Org mode version 9.4.4 (release_9.4.4 @ /usr/local/share/emacs/28.0.50/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-agenda-files '("~/org/nested.org")
 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-todo-keywords '((type "TODO(t)" "STARTED(s)" "UNSTARTED(u)" "|" "DONE(d)") (type "PENDING(p)" "HOLD(h)" "ONGOING(o)" "|" "DONE(d)")
		     (sequence "|" "CANCELED(c)" "ABSTAINED(a)"))
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 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-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) ("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)
		       ("file" :complete org-link-complete-file) ("elisp" :follow org-link--open-elisp) ("doi" :follow org-link--open-doi))
 org-metaup-hook '(org-babel-load-in-session-maybe)
 )