Deep Research Formatter

Deep Research Formatter is an Obsidian plugin for cleaning Markdown exported from ChatGPT Deep Research.

Deep Research exports often contain inline marker tokens such as citation, entity, and URL annotations that are readable inside ChatGPT but noisy in plain Markdown. This plugin removes or rewrites those markers so the document is easier to read in Obsidian, including both private-use marker wrappers and exported 【...†...】 citation blocks.

What it does

• Removes cite markers entirely.
• Removes exported 【...†...】 citation blocks entirely.
• Replaces entity markers with their readable label.
• Replaces url markers with their readable label.
• Falls back safely for unknown marker types when possible.
• Preserves YAML frontmatter, fenced code blocks, and inline code.
• Applies only minimal whitespace cleanup after marker removal.

Requirements

• Node.js 20 or later
• npm 10 or later
• Obsidian 1.5.0 or later

Project layout

• src/: plugin source code
• tests/: automated tests
• manifest.json: Obsidian plugin manifest
• versions.json: Obsidian version compatibility map
• main.js: compiled plugin entry file

Install dependencies

npm install

Build

Create a production build:

npm run build

This compiles the plugin to main.js in the repository root and the CLI to dist/cli.js.

Development

Start esbuild in watch mode:

npm run dev

Run the automated tests:

npm test

If you also want a TypeScript-only check:

npx tsc --noEmit

Install into Obsidian

1. Build the plugin with npm run build.
2. Open your Obsidian vault folder.
3. Create this plugin directory if it does not already exist:

<your-vault>/.obsidian/plugins/deep-research-formatter/

4. Copy these files into that directory:

main.js
manifest.json
versions.json

5. In Obsidian, open Settings -> Community plugins.
6. Turn off Restricted mode if needed.
7. Enable Deep Research Formatter.

Usage

Open a Markdown note exported from Deep Research, then use the Command Palette in Obsidian.

Available commands:

• 清理当前笔记中的 Deep Research 标记
• 清理当前选区中的 Deep Research 标记

Command behavior:

• The first command cleans the entire active Markdown note.
• The second command cleans only the current editor selection.
• If no Deep Research markers are found, the plugin shows a notice and does nothing.

CLI usage

You can also format a vault directory, or any subdirectory inside it, from the command line:

npm run format:vault -- /path/to/your/vault

CLI behavior:

• Recursively processes .md files under the target directory.
• Skips .obsidian/, .git/, and node_modules/.
• Rewrites only files whose content actually changes.
• Prints a summary of scanned files, updated files, failures, and marker counts.
• Returns exit code 1 for invalid arguments and 2 when one or more files fail to process.

Show the CLI help text:

npm run format:vault -- --help

Current marker handling

The current implementation recognizes the marker wrapper used in Deep Research exports and handles these marker types:

• cite: removed
• 【...†...】 citation blocks: removed
• entity: replaced with readable text
• url: replaced with readable text
• unknown tags: best-effort readable fallback, otherwise removed

Notes

• This plugin is intentionally conservative. It does not try to reformat the whole Markdown document.
• It focuses on Deep Research marker cleanup only.