SideNote2 is an Obsidian plugin for side comments that stay attached to the note.

It is built for a minimal workflow: humans work in the sidebar, while agents can read the same comments directly from the markdown file. Inspired by mofukuru/SideNote.

• Uses a dedicated sidebar for drafting, editing, resolving, reopening, and deleting comments.
• Supports Obsidian-style [[wikilinks]] inside side comments to link existing notes or create new markdown notes.
• Type # in a side note to search existing tags or add a new one.
• Keeps resolved comments archived instead of removing them.
• Generates SideNote2 index.md as a vault-wide comment index.
• Lets the index sidebar switch between the comment list and a thought-trail graph built from side-note wiki links. The graph follows those links across connected markdown files, so it can show multi-step trails instead of only direct one-hop links.
• Supports agent workflows so Codex, Claude Code, and other assistants can read and update side comments from the note-backed storage format.

1. Install BRAT settings -> install community plugins -> BRAT
2. Install the SideNote2 beta Open BRAT, enable Auto update if you want, then add the plugin as shown below.

   

3. If you want Codex to expose SideNote2 as a skill in /skills, ask Codex to install it directly from the GitHub skill URL:

Use the skill-installer skill and install:
https://github.com/vicky469/SideNote2/tree/main/skills/sidenote2

4. Restart Codex, then run /skills. You should see sidenote2.

1. Select text in a note.
2. Right-click Add comment to selection. You can use the ribbon button to open the sidebar, or assign your own hotkey in Obsidian.
3. Write the comment in the sidebar. See Writing in Side Notes below for editor shortcuts and formatting behavior.
4. Review it later from the sidebar, from SideNote2 index.md, or from the sidebar thought trail.

For power users:

Agents can read, add, update, resolve the side notes from markdown.

In Codex CLI, Claude Code, or another assistant, you can ask:

Show me the side comment for "selected text" in "/Users/path/to/note.md".

Or update it:

Update the side comment for "selected text" in "/Users/path/to/note.md" to:
Your new side comment text here.

If multiple side comments in the same note use the same selected text, include a little more nearby context or the comment id.

• Index header image URL
• Index header image caption
• Debug mode This is not implemented yet.

• SideNote2: Add comment to selection
• SideNote2: Sync AGENTS.md in vault root
• SideNote2: Remove SideNote2 agent support from vault

Before uninstalling SideNote2, remove its managed agent-routing block from the vault.

Press Command + P to open the command palette, then run:

• SideNote2: Remove SideNote2 agent support from vault

Then uninstall the plugin from Obsidian.

This removes only SideNote2's managed AGENTS.md instructions. Stored side comments remain in the markdown notes until you edit or remove them separately.

For MD files: Each note stores its comments in a trailing hidden <!-- SideNote2 comments --> JSON block inside the same markdown file.

For PDF files: The JSON block is stored in plugin data.

SideNote2 index.md is just a generated index, not separate storage.

Setup, local vault install, debugging, and architecture notes live in README-dev.md.

• Added a settings shortcut to sync or remove SideNote2's managed vault AGENTS.md block so uninstall cleanup is easier to discover before removing the plugin.
• Clarified the README and dev docs so the sidenote2 Codex skill and the vault AGENTS.md routing are documented as separate pieces of the agent workflow.

• SideNote2 now manages a vault-root AGENTS.md block automatically so Codex and other assistants can route obsidian://side-note2-comment?... links, replies, updates, and resolves back to the note-backed source of truth.
• Added manual Sync AGENTS.md in vault root and Remove SideNote2 agent support from vault commands, plus bundled CLI support for uninstalling the managed vault instructions and resolving stored comment threads.
• Refined the index sidebar list and thought-trail tabs so the toolbar state is clearer and targeted reply reveals keep the thread expansion state users expect.
• Updated the architecture examples and workflow docs to match the current threaded note model and the built-in agent-routing flow.

• Threaded replies in the index sidebar now render as their own nested comment cards instead of being flattened into the parent card body.
• Added a top-level index toggle to show or hide child replies, while still auto-showing them when a targeted reply is opened for reveal or edit.
• Improved sidebar thread actions and metadata presentation so parent and child cards behave more consistently in index view.
• Fixed bundled sidenote2 CLI command output so agent and automation workflows can reliably capture success and error messages.

• SideNote2 now auto-migrates older flat note comments to threaded entries[] storage on startup after the upgrade, including vaults coming forward from older 1.x builds such as 1.0.32.
• No manual migration step is required for normal users. Open the vault in SideNote2 2.0.1 and the plugin handles the legacy note-comment upgrade in the background.
• This automatic migration bridge is temporary and will be removed in a later release after the 2.0.1 upgrade window.

• Breaking: SideNote2 introduced threaded note-backed comments with entries[] instead of the older flat comment payload.
• Current versions handle that older note upgrade automatically on startup, so users on 2.0.1+ do not need to run a manual migration command.
• Added append-to-thread comment helpers for agents and repo automation via npm run comment:append and scripts/append-note-comment-entry.mjs.
• Improved note comment rendering and index workflows, including safer CLI writes, better index sidebar behavior, and page-note previews in the generated index note.

MIT