Skill v3.0.0

name: org-ecosystem description: Use for Org-mode, covering org files, syntax, babel, export, agenda, capture, GTD, literate programming, and publishing workflows. version: 3.0.0

Org-mode workflows for GTD, literate programming with Babel, and export/publishing. Assumes familiarity with headlines, basic markup, and standard block types — this covers the parts of Org that surprise or bite: timestamp semantics, Babel's execution/security exposure, capture-template mechanics, and export/agenda traps.

Timestamps and repeaters

Active <...> timestamps appear in the agenda; inactive [...] timestamps do not. This is the only functional difference between the two syntaxes — get it backwards and TODO items go missing from the agenda, or bookkeeping timestamps start cluttering it.

Repeater cookies change what "next occurrence" means, not just the interval:

• +1w — jumps straight to now + 1 week, skipping any missed occurrences.
• ++1w — cumulative: advances one interval at a time from the original date until the result is

in the future, so a task missed for a month advances four separate weeks rather than jumping straight to "next week from today."

• .+1w — resets from the completion date rather than the original schedule; use for tasks like

"review again in a week" where drift shouldn't compound.

TODO states and capture

#+TODO: TODO(t) NEXT(n) WAITING(w@/!) | DONE(d!) CANCELLED(c@)

@ prompts for a note on state change, ! logs a timestamp; w@/! logs a note on entry and a timestamp on exit. States left of | are open, right of | are done — stuck-project detection and clock reports key off this partition, not off individual state names.

Capture placeholders: %? cursor position, %i captured region, %a link back to the capture origin, %U/%T inactive/active timestamp. %a is the one worth flagging — it silently embeds a link to wherever point was when capture fired, useful for provenance but a dangling or absent link when capture is triggered from a scratch buffer.

Babel: execution and security

(setq org-confirm-babel-evaluate nil)

This disables the per-block confirmation prompt before evaluating code. Once set, C-c C-c inside any source block — or an export that triggers evaluation, depending on :eval — runs arbitrary shell/python/elisp with no gate. Treat .org files from untrusted sources as executable, not as documents; scope org-confirm-babel-evaluate per-directory with .dir-locals.el instead of disabling it globally if you ever open files you didn't author.

A block only executes if its language was loaded via org-babel-do-load-languages; a #+BEGIN_SRC ruby block with ruby absent from that list fails with "no org-babel-execute function for ruby" even though the syntax highlights fine — check the loaded-languages list before assuming a broken block is a syntax problem.

:session keeps a REPL alive across blocks, so state leaks between blocks sharing a session name — a variable set in a later block is visible to an earlier one if that earlier block re-runs. :noweb yes expands <<name>> references at tangle or execute time, not at edit time, so the buffer's visible content and its executed content can diverge.

Tangle and noweb

:mkdirp yes creates parent directories on tangle; omit it and tangling into a nonexistent directory fails outright. Noweb references (<<name>>) resolve against blocks carrying a matching :noweb-ref, not against #+NAME: — confusing the two is the usual reason a tangled file still contains a literal <<placeholder>>.

Export

H:N in #+OPTIONS sets which heading level becomes a Beamer frame boundary — it is easy to assume H: maps to LaTeX's \section depth the way it does for other backends, but for Beamer it controls frame splitting instead.

org-latex-pdf-process runs an external shell command sequence (latexmk, optionally -shell-escape); the same untrusted-content caution as Babel applies when -shell-escape is enabled, since LaTeX can execute code under that flag too.

:noexport: tags and #+BEGIN_COMMENT blocks are excluded from export output but still parsed — a :noexport: heading with a live source block still executes on C-c C-c and still executes during export-triggered evaluation; it just never appears in the rendered document.

org-cite (built into Org since 9.5, bundled with Emacs 30.2) replaces org-ref. The two conflict on citation-key parsing when both are loaded, so migrate rather than running them side by side.

Agenda performance

org-agenda-files is scanned in full on every agenda build — there is no incremental index — so a large or deeply nested file set makes every org-agenda-custom-commands invocation noticeably slower. Point it only at files that actually carry schedulable items, not at an entire notes tree.

Refile

(setq org-refile-allow-creating-parent-nodes 'confirm) lets refile create a new heading on the fly. Setting it to t instead of 'confirm means a typo in the refile target silently creates a stray heading rather than prompting first.

org-roam

(use-package org-roam
  :ensure t
  :custom
  (org-roam-directory (file-truename "~/org/roam/"))
  (org-roam-completion-everywhere t)
  :config
  (org-roam-db-autosync-mode))

org-roam-db-autosync-mode keeps the SQLite cache in sync only with edits made through Emacs. Changes from outside Emacs — another editor, a script, git checkout — do not trigger a resync; run org-roam-node-sync/org-roam-db-sync explicitly afterward, or node lookups silently return stale results.

Related

• emacs-ecosystem — Emacs Lisp mechanics (use-package, hooks) that

org-mode customization is built on.

• serena-usage — symbol operations for navigating org structures

programmatically.

• context7-usage — fetch current Org-mode documentation when a

pattern here may be stale against the latest release.

• technical-documentation — documentation patterns

applicable to org export output.