✅ Folding and Visibility

✅ Headings

✅ Org-Mode Heading Navigation

✅ Granular Addressing (Anchors)

These commands implement granular addressing: pointing a link at a location finer than a heading. An anchor is a native org target (<<name>>), radio target (<<<name>>>), or #+NAME: keyword. Because the anchor lives in the text, it travels with its content when you move a paragraph and disappears with it when you delete one (the link then becomes a detectable orphan). Anchors are indexed in the scimax database, so [[name]] links resolve across files and back-links are tracked at the object level.

Following a [[name]] link first searches the current file, then falls back to the database to resolve an anchor of that name anywhere in the workspace.

✅ Dialog Notes

Attach a decision, question, or comment to a passage. A note is an org footnote with a note- label prefix, collected under a * Notes :noexport: section and excluded from exports. See Dialog Notes.

Crucible Knowledge Bases

Browse and search crucible wikis, and show the graph around an article. See Crucible Knowledge Bases.

✅ DWIM Commands

✅ Org Utility Commands

✅ Lists

Commands for manipulating org-mode and markdown lists.

✅ TODO Keywords

✅ Task Dependencies

Express dependencies between TODO tasks (org-depend style). See Task Dependencies for the full guide.

✅ Project Management

Task tables, a project view with a Gantt chart, a dependency graph, and a people database. See Project Management for the full guide.

Contacts & Entities

Fuzzy-pick a tagged/propertied heading (contact, location, reagent, …) and act on it. See Contacts, Locations & Entity Selector.

✅ Checkboxes

✅ Markdown Tasks

✅ Basic Table Operations

✅ Row and Column Operations

✅ Advanced Table Operations

✅ Table Formulas

✅ Basic Babel Operations

✅ Advanced Babel Operations (scimax-ob)

Extended Babel Features

✅ Export Dispatcher

Org Preview

Live rendered preview of an org file. See Org Preview.

✅ HTML Export

✅ LaTeX/PDF Export

LaTeX Build Profiles

Named sequences of build commands (pdflatex+bibtex, lualatex+biber, ...) defined in latex-profiles.json or settings. See Build Profiles documentation.

Other Export Formats

✅ Markdown File Export

Export markdown (.md) files to other formats via Pandoc. Complements the org-to-markdown export above — these commands operate on markdown source files.

Requires Pandoc to be installed on the system.

PDF export uses xelatex by default (scimax.markdown.export.pdfEngine), so characters typed directly in the text, such as ′, → or Greek letters, are typeset rather than stopping pdflatex with "Unicode character not set up for use with LaTeX". The body font is scimax.markdown.export.mainFont; left empty, it is Arial Unicode MS on macOS, which has these characters, and Pandoc's default font elsewhere. A mainfont: in the document's YAML front matter takes precedence. If the font lacks some characters, the PDF is still written without them, and a warning names them.

Markdown Preview

Reveal scrolls the Markdown preview (opening one if needed) to the cursor line. For the other direction, double-click the preview. Refresh re-renders the Slide Sorter, for example after editing a theme file. See Marp Slides.

✅ Jupyter Notebook Export

Export org documents to Jupyter notebook (.ipynb) format.

✅ Clipboard Export

Copy document content to clipboard in various formats for pasting into other applications.

Email Heading

Compose an email from the heading at point, record a Gmail link to it, and optionally mark the heading done. See Email a Heading.

Custom Exporters

User-defined export backends using Handlebars templates. See Custom Exporters documentation.

Loaded exporters are also listed in the export dispatcher (C-c C-e) under [c 1], [c 2], ..., with [c c] opening the picker.

✅ Clocking

Time tracking commands for measuring effort on tasks.

Clock entries are stored in a :LOGBOOK: drawer under the heading. Use scimax.org.clockReport to generate a summary of time spent.

Agenda Views

Advanced Agenda

✅ Basic Journal Operations

Journal Utilities

✅ Basic Database Operations

Advanced Search

✅ Semantic Search (AI)

✅ Database Maintenance

✅ Link Graph Visualization

Commands for visualizing file connections through links.

✅ Troubleshooting and Diagnostics

Commands for debugging issues and reporting problems.

AI Agent Skills

Install the bundled scimax skills for Claude Code, VS Code (GitHub Copilot), Codex, Cursor and other agents. See CLI: Skill.

Citation Management

✅ Citation Editing

✅ Bibliography Management

✅ OpenAlex Integration

✅ BibTeX Speed Commands

Speed commands for BibTeX files, active at column 0 of @entry lines.

Fuzzy Search (Swiper)

✅ Jump (Avy)

✅ Recenter

Emacs-style recenter-top-bottom. Pressing C-l repeatedly while the cursor stays put cycles the cursor line through three scroll positions: center on the first press, top on the second, bottom on the third, then back to center. Moving the cursor or switching editors resets the cycle to center.

✅ Mark Edits

✅ Review Edits

✅ Navigation

Visibility

✅ Structure Editing

✅ TODO and Tags

✅ Scheduling and Timestamps

✅ Properties and Clocking

✅ Archiving

✅ Help

Section Navigation

✅ Environment Navigation

✅ Structure Editing

Environment Manipulation

✅ Compilation and PDF Viewing

✅ Error Navigation

✅ Insertion Commands

✅ Utilities

✅ Speed Commands

Speed commands are available when cursor is at the beginning of a section line.

Section speed commands (at \section, \subsection, etc.):

• n :: Next section

• p :: Previous section

• f :: Next sibling

• b :: Previous sibling

• u :: Parent section

• j :: Jump to section

• L :: Promote section

• R :: Demote section

• U :: Move section up

• D :: Move section down

• m :: Mark section

• k :: Kill section

• c :: Clone section

• i :: Insert section

• Tab :: Toggle fold

✅ Environment Speed Commands

Environment speed commands available at \begin{...} lines.

Environment speed command keys:

• n :: Next environment

• p :: Previous environment

• j :: Jump to environment

• s :: Select environment

• c :: Change environment

• k :: Kill environment

• w :: Wrap in environment

• u :: Unwrap environment

• * :: Toggle star

• l :: Add label

• C :: Add caption

• i :: Environment info

Inline LaTeX Previews

✅ LaTeX Cache Management

Insert Templates

New Files from Templates

✅ Template Management

✅ Kernel Management

✅ Most Common Keybindings

✅ Export Keybindings

Babel/Source Block Keybindings

✅ Project and Navigation Keybindings

scimax.help.describeCommand

Shows the keybindings for a specific command. Useful for learning keyboard shortcuts.

scimax.help.describeKey

Describes what a specific key combination does. Enter the key sequence to see its bound command.

scimax.help.listKeybindings

Lists all keybindings defined by the extension. Opens a quick pick to browse available shortcuts.

scimax.help.describeVariable

Browse all scimax settings with completion. Shows the setting type, default value, current value, and description. Select a setting to open VS Code Settings.

scimax.help.apropos

Search the documentation for keywords. Enter search terms to find relevant documentation sections. Results are ranked by relevance (headings, commands, keybindings, content). Select a result to view details or open the documentation file.

✅ scimax.update

Update Scimax VS Code from GitHub releases. This command:

1. Fetches the latest release from the GitHub repository

2. Shows the current version vs. the latest available version

3. Downloads the VSIX file with progress indication

4. Installs it using VS Code's extension manager

5. Offers to reload VS Code to activate the new version

This provides an easy way to update without leaving VS Code. Requires the repository to have GitHub releases with VSIX files attached.

scimax.org.lint

Runs the org-mode linter on the current document. The linter checks for:

• Duplicate IDs

• Broken internal links

• Missing TODO keywords in sequences

• Unbalanced brackets and quotes

• Invalid timestamps

• Missing required properties

• And more

Results appear in the Problems panel.

scimax.org.lintCheckers

Shows available lint checkers and allows enabling/disabling specific checks.

✅ Mark Ring Concepts

• *Mark*: A saved cursor position that you can return to

• *Point*: The current cursor position

• *Mark Ring*: A stack of marks (per-document), most recent first (default size: 16)

• *Global Mark Ring*: A cross-file stack of marks for navigating between documents

• *Selection Mode*: When mark is set, cursor movement extends the selection from the mark

✅ Common Workflows

How It Works

C-y inserts the entry under the yank pointer, which is normally the newest kill. Pressing M-y straight after a yank replaces the yanked text with the next older kill, and each further M-y steps back one more, wrapping around at the oldest. The status bar shows which entry you are on (for example Kill ring: 3/12). Once you move the cursor or edit, M-y instead opens a picker over the whole ring: type to filter, press Enter to insert, or click the trash icon to drop an entry. Whichever entry you insert becomes the one the next C-y yanks.

Consecutive kills at the same spot join into one entry, as in Emacs, so pressing C-k three times and then C-y brings back all three lines. A kill made after you move the cursor or edit starts a new entry.

Text copied elsewhere (in another application, or with Cmd+C) is pulled onto the ring before the next kill or yank, so it is not lost when a kill replaces the clipboard. The ring holds 120 entries by default (scimax.killRing.maxSize) and is not saved between sessions.

These commands push onto the ring: C-k (scimax.killLine), C-w, M-w, killing or copying an org subtree or source block, killing a LaTeX section or environment, killing or copying a BibTeX entry, the jump kill-line and copy-line actions, and rectangle kill and copy. Rectangle yank (C-x r y) still inserts the last killed rectangle as a rectangle.

Auto-Copy (Copy on Select)

Text you highlight with the mouse (drag, double-click a word, triple-click a line) is copied to the system clipboard and pushed onto the kill ring as soon as you let go, like copy-on-select in a terminal. A notification in the lower right shows what was copied and closes itself after two seconds (turn it off with scimax.autoCopy.notify). Paste it with Cmd+V or C-y. The clipboard you had before is not lost: it is pulled onto the ring first, so M-y gets it back.

Only mouse selections are copied. Regions made with Shift+arrows or C-SPC are left alone, so selecting with the keyboard and pasting over the selection still works. If you highlight with the mouse and then press Cmd+V, you paste the highlighted text back over itself; use M-y to pick the older entry instead.

It is on by default. Turn it off with scimax.autoCopy.enabled set to false, or flip it with the command below.

Related Topics

• Keybindings - Kill Ring keys

• Mark Ring - setting the region with C-SPC

• Configuration - scimax.autoCopy.enabled

• Configuration - scimax.killRing.maxSize

• Timestamps show how long ago each mark was set

✅ Rectangle Concepts

• *Rectangle*: A column-aligned region of text defined by two corners (the selection's anchor and active positions)

• *Rectangle Clipboard*: A separate clipboard (not the system clipboard) that stores the last killed/copied rectangle. This matches Emacs behavior.

• *Kill*: Delete the rectangle and save it to the rectangle clipboard

• *Yank*: Insert the rectangle clipboard contents at the cursor position

✅ Common Workflows

✅ Related Topics

• Keybinding Reference: Rectangle Commands

• Hydra Menus - Rectangle commands are available in the Hydra menu system

Setting Up a Publishing Project

1. Run scimax.publish.init to create a publishing configuration

2. Configure the project in the generated .org-publish.json file

3. Use scimax.publish.project to publish the configured project

Publishing Configuration

The .org-publish.json file configures:

• Source directory for org files

• Output directory for HTML

• Include/exclude patterns

• HTML template settings

• Asset handling (CSS, images)

Dired Commands

Dired (Directory Editor) provides Emacs-style file management. Open with C-x d and use these keys in the dired panel:

• Navigation: n/p (next/prev), RET (open), ^ (parent), g (refresh)

• Marking: m (mark), u (unmark), U (unmark all), t (toggle marks)

• Operations: D (delete), C (copy), R (rename/move), + (create directory)

• WDired: C-x C-q (enter edit mode), C-c C-c (commit), C-c C-k (cancel)

See Dired documentation for full details.

scimax.replaceNonAscii

Replaces common non-ASCII characters (smart quotes, em-dashes, etc.) with their ASCII equivalents. Useful for preparing documents for systems that don't handle Unicode well.

scimax.showDebugInfo

Displays diagnostic information about the scimax extension, including version, enabled features, and configuration state. Useful for troubleshooting.