The Archive (native)

• Plain-text Zettelkasten app with wiki-links, fast search, and minimal UI. File-based (markdown), local-first. The primary tool for this zettelkasten. (Workflow context)

  • My current or previous usage of the app.

    • Primary zettelkasten tool – all permanent notes live here. Main journaling and thought capture. Search and browse the knowledge network. Private notes hidden from published site. (Content pipeline)

    • Part of three-tool thinking system: Zettelkasten (The Archive) for journaling and permanent notes, TaskPaper for planning/brainstorming, Emacs for code experiments. (Different thinking modes)

• Articles and websites

  • Book workflow, introduction to The Archive, saved searches

  • How to Do Research with The Archive

  • A love letter to The Archive

    • Summary of this article.

      • Manan Khattar’s case for The Archive: 1,330 notes (350K words) in plain text. Speed and keyboard-centric design minimize cognitive friction. Search-driven workflow enables queries like #literature #inbox (productivity OR writing) (202407 OR 202408). Native Zettelkasten support from zettelkasten.de’s creator.

      • Trade-offs acknowledged: unique identifier requirement makes wikilinks less readable than Obsidian. No plugin system—requires Alfred workflows for full functionality. No mobile app (uses 1Writer as workaround).

      • Core thesis: tool choice matters less than sustaining writing-focused thinking habit. The Archive’s speed accelerated his adoption.

      • I got to know kindaVim from this article.

        • Actually, I already wrote about this before: Bookmarked “kindaVim”

        • There are videos about kindaVim: kindaVim – YouTube

          • Most of them just ramblings.

        • This is another app from the same guy for keyboard based UI navigation: Wooshy

iA Writer (native)

• Distraction-free markdown editor with focus mode, syntax highlighting, and publishing integrations. Typography-first design from Information Architects.

  • My current or previous usage of the app.

    • Drafting and linking workflow via smart folders. #Drafting folder shows notes being written, #Linking folder shows notes ready for outline placement. The final drafting step before zettelkasten integration. (Content pipeline)

• Articles and websites

  • How I set up iA Writer After Moving from Ulysses

  • Writing Workflow – Stuart Lennon

    • Summary of the article, focusing on the question “What am I writing?” section.

      • Stuart Lennon’s framework: three writing categories.

      • Longform (2000+ words) in Scrivener for novels/non-fiction.

      • Shortform drafts in iA Writer for blog posts and reports.

      • Notes ideas in Obsidian for thoughts not yet publication-ready.

      • The “What am I writing?” question determines tool selection. Plain text everywhere for portability. DEVONthink as archive. Open question: whether Drafts could serve as unified entry point with automated routing.

Bike (native)

• Native macOS outliner with fast keyboard navigation, collapsible hierarchy, and scripting support. Version 2 adds extensions API and custom attributes. The app running this outline.

  • My current or previous usage of the app.

    • Core organizing tool for the content pipeline. Ideas get arranged in Bike outlines before export to zettelkasten via Drafts. Also manages the folgezettel outline structure. (Content pipeline)

    • Decoding files are raw Bike outlines for blog posts. All content ready for publishing; private things go to interstitial journal instead. (Journal-type apps)

    • Now used as AI-integrated thinking space with thread-watch and MCP server. Reactive prompting via @question attributes. (Bike thinking tool exploration)

• Articles and websites

  • Bike: An Elegant Outliner For Mac-Focused Workflows – MacStories

  • Bike: Tool for thought

TaskPaper (native)

• Plain-text task management using indentation and tags. Same developer as Bike. Good for project brainstorming and task breakdown. (Workflow context)

  • My current or previous usage of the app.

    • TaskPaper role: plain-text planning and brainstorming for project-specific thinking and task breakdown. OmniFocus shortcut triggers “project brainstorming” in TaskPaper. (Different tools for different thinking modes)

    • Historical use: interstitial journaling. Deprecated that role, moved journaling back to zettelkasten. Brainstorm sessions now live in the journal rather than separate files. (Plans for TaskPaper changes)

    • Workflow: Bike for initial outlining, switch to TaskPaper once plan solidifies. Part of the plain-text system alongside The Archive and Bike. (Text-based system)

• Articles and websites

  • TaskPaper for Mac

  • How do you use TaskPaper? – Forum Discussion

  • The move to a plaintext GTD system

Drafts (native)

• Quick capture app with powerful actions system for routing text to other apps. Automation-first design. Inbox for thoughts, not storage.

  • My current or previous usage of the app.

    • Export gateway from Bike to zettelkasten. Ideas organized in Bike get exported through Drafts into new notes. Also used for quick capture on Apple Watch at night. (Content pipeline)

    • MCP server spec exists for automation integration. AppleScript-based CRUD operations planned but automation permissions need resolution first. (Drafts MCP spec)

• Articles and websites

  • Automating Email with Drafts (feat. David Sparks)

  • Quick Capture with Drafts – The Sweet Setup

  • A Drafts Workflow for Conferences

Craft (native)

• Block-based document editor with rich formatting, folder structure, and cross-device sync. Apple Design Award winner, positioned between Notion and traditional notes.

  • My current or previous usage of the app.

    • Primary reading queue manager via Readwise-Craft syncer integration. Articles flow in, get processed with highlights, then export to zettelkasten. MCP server enables AI automation. (Readwise-Craft syncer)

    • Daily notes workflow for session logging and project tracking. Block-based structure good for moving content between documents. (Content pipeline)

• Articles and websites

  • Second Brain Workflows (Obsidian vs Craft for PKM)

  • How I’m Using Craft in My Productivity Workflows

  • The Craft App — A Year of Magical Linking

DEVONthink (native)

• Document/knowledge management database with AI classification, OCR, and smart groups. Stores anything, indexes everything. Research-grade organization.

  • My current or previous usage of the app.

    • DEVONthink role: document archive and reference storage. Articles, PDFs, web archives, receipts. AI classification and OCR. Research-grade organization with smart groups. (Incremental reading system)

    • Reading queue integration: documents captured to DEVONthink appear in OmniFocus @Read/Review perspective. The queue is in OmniFocus, content stays in DEVONthink.

    • MCP access via mcporter enables AI agents to search and retrieve DEVONthink content. Source references in older zettelkasten notes use x-devonthink-item:// links.

• Articles and websites

  • Use Obsidian and DEVONthink Together!

  • DEVONthink for Historians: developing your qualitative research process

  • Four Hour Setup: How I use DEVONthink

  • Workflows for Scholars – DEVONtechnologies

Obsidian (Electron)

• Plugin-extensible markdown vault with graph view, backlinks, and community ecosystem. Electron-based, local files. Power-user PKM tool.

  • My current or previous usage of the app.

    • Limited use currently. Explored for AI integration with Cursor but zettelkasten workflow remains in The Archive. Considered for consolidating Planning folder but not active. (Obsidian exploration)

• Articles and websites

  • How to Connect Zotero and Obsidian for the Ultimate PhD Workflow

  • How to Build a Second Brain in Obsidian: Complete Setup Guide

  • PKM + Obsidian: The Tech Stack for Your Brain

OmniOutliner (native)

• Professional outliner from OmniGroup with styling, columns, and export options. More structured than Bike, less nimble. AppleScript support.

• Articles and websites

  • GTD = OmniFocus + OmniOutliner + DEVONThink

MindNode (native)

• Visual mind mapping with clean design and focus mode. Exports to various formats. Good for brainstorming spatial relationships, less for linear text.

  • My current or previous usage of the app.

    • Used for preparing content before processing. Ideas get connected to mindmaps with tags and links before moving to notes. Public mindmaps shared online (e.g., Japanese Design and Aesthetics). (Processing workflow)

• Articles and websites

  • How David Develops with Mind Maps

Scapple (native)

• Freeform note board from Literature and Latte (Scrivener makers). Spatial arrangement of text snippets with connection lines. Idea exploration before structure.

• Articles and websites

  • Scapple: a great little brainstorming gem

  • How to Get Unstuck + Plot Your Novel in Scapple

NotePlan (native)

• Markdown notes with calendar integration and task management. Daily notes workflow with backlinks. Hybrid of journaling and task app.

• Articles and websites

  • My Ultimate Productivity Tool Workflow for 2024: Plan with Me in NotePlan

  • My Productivity Workflow 2025: Task Management + Apple Shortcuts + Gmail

  • My NotePlan Workflow — Everything I Need to Plan and Execute my Day

  • NotePlan: Your Notes, Tasks, and Calendar in One Place – MacSparky

Distill (Tauri)

• AI-native thinking tool with append-only threads and contextual awareness. Local-first with cloud sync. Discussed earlier in this document.

  • My current or previous usage of the app.

    • Explored briefly – app installed, bug filed about quick capture window positioning with right-side Dock. Append-only threading concept influenced thread-watch development. (Reactive prompting)

    • Removed from active toolchain – no current use case. Keep app installed for existing content. (Journal-type apps conclusion)

    • Explored briefly – app installed, bug filed about quick capture window positioning with right-side Dock. Append-only threading concept influenced thread-watch development. (Reactive prompting)

    • Removed from active toolchain – no current use case. Keep app installed for existing content. (Journal-type apps conclusion)

• Articles and websites

  • Active intelligence – Distill Documentation

  • Workflows – Distill Documentation

Bear (native)

• Markdown notes with tags, nested tags, and backlinks. Clean native UI. Simpler than Obsidian, more polished than most.

• Articles and websites

  • How I use Bear As My Second Brain With Alfred

  • Bear is a fully fledged writing app – experiences as former Ulysses user

  • Workflow wobbles – Stuart Lennon

Ulysses (native)

• Long-form writing app with library management and publishing targets. Markdown-based but hides syntax. For writers shipping manuscripts.

• Articles and websites

  • How I Organise My Writing

  • A Complete Ulysses Writing Workflow – The Sweet Setup

  • Choosing Ulysses over PKM Software for Longform Writing

Noteship (native)

• Minimal sticky-note style capture app. Menu bar access, quick entry. Capture-focused, not organization-focused.

• Articles and websites

  • Noteship User Guide

  • Meeting Notes with Noteship

Notebooks 3 (native)

• Hierarchical notebook app with nested books and markdown support. Cross-platform sync. Traditional notebook metaphor with modern features.

• Articles and websites

  • Ten Reasons I Write Everything in Notebooks App

  • Task Management in Notebooks

Scrivener (native)

• Long-form writing IDE with binder, corkboard, and compile system. For novels, screenplays, research papers. Structure-first drafting.

• Articles and websites

  • My Easy Scrivener Writing Workflow + Setup

  • How to Use Scrivener Like a PhD Student

  • How I Use Scrivener For Fiction And Non-Fiction – The Creative Penn

  • Structuring your novel in Scrivener

Tinderbox (native)

• Hyper-customizable note database with agents, attributes, and visual maps. Steep learning curve, extreme power. For complex knowledge work and research.

  • My current or previous usage of the app.

    • Higher-level life management – dreams, someday/maybe ideas, things above projects. Scripts connect OmniFocus to Tinderbox for two-way sync. Ideas and goals live here; projects get managed in OmniFocus. (Tinderbox for life management)

    • Incremental Reading document watches Readwise chunks folder. Considered skipping from general chunk processing due to workflow friction getting content in. (Tinderbox workflow friction)

• Articles and websites

  • Working with Tinderbox Zotero

  • PhD Tools: Think better with Tinderbox

  • Tinderbox for writing long Academic texts – Forum

BBEdit (native)

• Professional text editor with grep, syntax coloring, and scripting. Not a note app per se – a text tool that handles notes. 30+ years of macOS development.

• Articles and websites

  • Taking Notes: BBEdit 14, Working Copy, Self-hosted Git Repo

  • BBEdit for Writers: A Guide and Appreciation

Org-mode with Emacs (native)

• Plain-text outliner inside Emacs with TODO states, scheduling, and literate programming. Keyboard-driven, infinitely extensible. Used for programming experiments. (Workflow context)

  • My current or previous usage of the app.

    • Current Emacs usage: Org Mode for programming experiments and literate programming. Still exploratory – set up OmniFocus shortcut for “programming docs” but workflow not fully established. (Different Tools for Different Thinking Modes)

    • Org Agenda navigation shortcuts documented separately – day/week views, date jumping, standard Emacs keybindings. (Org Agenda Shortcuts)

    • Position in tool ecosystem: Zettelkasten (The Archive) for journaling and permanent notes, TaskPaper for planning/brainstorming, Emacs for code experiments. Three tools, three thinking modes.

• Articles and websites

  • How I use Org-mode to organize my life

  • How I use Org Mode – Bill de hÓra

  • Getting Things Done with Emacs: Manage your life with Org Mode

Strflow (native)

• Stream-of-consciousness capture app with AI integration. Continuous text flow rather than discrete notes. Early-stage product.

  • My current or previous usage of the app.

    • Short idea dumps when thinking about something – ideas then move to OmniFocus/Bike. Removed from active toolchain; no current use case. App kept installed for existing content. (Journal-type apps conclusion)

    • Short idea dumps when thinking about something – ideas then move to OmniFocus/Bike. Removed from active toolchain; no current use case. App kept installed for existing content. (Journal-type apps conclusion)

• Articles and websites

  • Show HN: Strflow – Note-Taking for people who keep abandoning notes

  • Strflow — Note-Taking, Like Chatting

NotePlus (native)

• Native macOS LLM client (~10MB). Supports OpenAI, Gemini, Anthropic, Ollama, DeepSeek, Copilot. Different category than Bike—this is a chat interface with note-taking features, not an outliner. The “True Native” claim positions it against Electron apps.