Taming Messy Notes with AI Terminal Agents

Note-taking has always felt slippery to me. Ideas land in half-finished drafts, todo lists live everywhere, and the moment I need a past thought it is buried three folders deep. The hard part is rarely capturing the note—it's grooming, connecting, and revisiting what I already wrote.

Recently I pulled two threads together: file-first note apps and AI assistants that run from the terminal. The combo has made maintaining my vault feel less like a chore and more like a routine I can stick with.

Start with files you control

Steph Ango, Obsidian's CEO, talks about the power of "file over app"—your work should live in portable files, not a hosted database. Obsidian embraces that idea: it is markdown files in folders, nothing more. When the notes are just files, any tool that speaks markdown can help.

Terminal agents speak the same language

Agents like Claude Code, Codex, OpenCode, and a wave of new CLI helpers work directly with the filesystem. They can read, diff, and edit local files the same way we do. Instead of a chatbot trapped in a browser tab, the assistant sits alongside your shell workflow.

Because both sides speak files, they naturally fit together: Obsidian (or any markdown-first app) manages the vault, while the agent brings structured help when I ask for it.

My vault workflow

Keep everything in plain markdown. I store notes in an
```
obsidian/
```
vault, but the approach works with any folder of
```
.md
```
files.
Open a terminal agent inside that vault.
```
cd ~/notes
```
followed by
```
codex
```
or
```
claude
```
drops the assistant into context. It instantly understands the folder structure and file contents.
Use lightweight commands as guardrails. Most agents support custom prompts—slash commands in Claude Code, recipes in Codex, macros elsewhere. I keep them in a
```
/commands
```
directory so the agent can reuse them.
Ask for focused help. I lean on the agent for repetitive organization, not for writing finished prose. It makes suggestions, links files, and summarizes, but I stay in control.

Commands that stick

These are the prompts that turned note maintenance from a weekly guilt trip into something sustainable:

```
/today
```
builds a daily note from a plain list of tasks, grouping them by project and linking to relevant docs.
```
/connections
```
scans the vault for related topics and proposes backlinks so the graph stays connected.
```
/sweep
```
finds stale notes—things I have not touched in ninety days—and drafts a quick summary so I can decide whether to archive or expand them.

Each command is just a small markdown file describing the job, the tone, and any folder rules. Because the assistant reads those files, it stays consistent without me rewriting the full prompt every time.

Why it works

Less switching. I stay in the editor and terminal I already use.
Lower friction. When cleanup is a conversation instead of a blank page, I actually do it.
Portability. If a new agent ships tomorrow, I point it at the same vault and reuse the prompts.

The result is not a perfectly automated system—it's still my messy brain—but the agent keeps the mess in motion. Notes feel alive again, and the daily sweep takes minutes instead of hours.

If note-taking feels like an endless backlog, try pairing a file-based vault with an AI terminal companion. Bring your own tools, keep your files close, and let the assistant shoulder the repetitive cleanup.