Suggest edit — Hermes Agent + Obsidian/IdeaFlow Second Brain Tutorial

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title: Hermes Agent + Obsidian/IdeaFlow Second Brain Tutorial
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# Hermes Agent + Obsidian/IdeaFlow Second Brain Tutorial

A beginner-friendly path for setting up a personal AI agent with a durable “second brain”: Hermes Agent does the work, IdeaFlow captures living thoughts and heartbeat triggers, and Obsidian / Markdown stores a browsable LLM Wiki you can keep improving over time.

> \[!info] Essential links
>
> * **Hermes:** [Desktop install](https://hermes-agent.nousresearch.com/desktop) · [setup docs](https://hermes-agent.nousresearch.com/docs/getting-started/installation) — start here; the install docs cover CLI/server setup too.
>
> * **Markdown tools:** [Obsidian](https://obsidian.md/) · [OpenMarkdownReader v1.0.15](https://github.com/tmad4000/OpenMarkdownReader/releases/tag/v1.0.15)
>
> * **IdeaFlow/workspace:** [IdeaFlow](https://ideaflow.io/) · [Cortex workspace](https://cortex.ideaflow.app/)
>
> * **Publishing + workflow:** [WikiHub](https://wikihub.md/) · [Farzapedia personal wiki skill](https://gist.github.com/farzaa/c35ac0cfbeb957788650e36aabea836d) · [IdeaFlow → Obsidian LLM Wiki skill](https://github.com/tmad4000/hermes-agent/blob/feat/ideaflow-obsidian-llm-wiki/skills/research/ideaflow-obsidian-llm-wiki/SKILL.md)
>
> * Meta: [Claw Camp Superconnector](http://clawcamp.superconnector.network/)
>
> * **ClawCamp contact / follow-up:** email [jacob+clawcamp@ideaflow.io](mailto:jacob+clawcamp@ideaflow.io) and [Jacob@ideaflow.io](mailto:Jacob@ideaflow.io). Use a subject that includes **“ClawCamp”** or **“ClawCamp second brain event”** so the message is easy to route/filter.
>
> * **Jacob LinkedIn:** [linkedin.com/in/jacobcolemit](https://linkedin.com/in/jacobcolemit)

## Start here: related pages

* [Privacy-Preserving Multi-Tier Hermes Bot Architecture](https://jacobcole.wikihub.md/architecture/wiki/hermes-multi-tier-bot-architecture) — architecture pattern for private, friend-facing, and sandboxed Hermes bots.

* [Vibe Coding Tutorial](https://jacobcole.wikihub.md/vibe-coding-tutorial) — beginner-oriented agent/workflow setup style.

* [AGI House LLM Wiki Guide](https://jacobcole.wikihub.md/@jacobcole/agi-house-llmwiki/index) — example of a personal/event LLM Wiki as a persistent knowledge base.

* [IdeaFlow → Obsidian LLM Wiki Hermes skill](https://github.com/tmad4000/hermes-agent/blob/feat/ideaflow-obsidian-llm-wiki/skills/research/ideaflow-obsidian-llm-wiki/SKILL.md) — the workflow skill for turning IdeaFlow / Thoughtstream notes into an Obsidian-compatible Knowledge Garden.

* Private WikiHub mirror of that skill: [@jacobcole/ideaflow-obsidian-llm-wiki](https://wikihub.md/@jacobcole/ideaflow-obsidian-llm-wiki).

## What you are building

By the end, you should have:

1. **Hermes Agent** installed locally or on a remote machine.
2. **A Markdown LLM Wiki** folder that acts as your durable knowledge base.
3. **Obsidian** or another Markdown reader to browse and edit the wiki.
4. **IdeaFlow / Thoughtstream heartbeat hooks** that let notes trigger useful agent actions.
5. **Hermes skills** that teach the agent how to find and maintain your wiki.

Think of this as three layers:

```text
Capture layer:      IdeaFlow / Thoughtstream notes, meetings, #tags, heartbeat
Agent layer:        Hermes Agent + skills + cron / heartbeat jobs
Knowledge layer:    Markdown LLM Wiki opened in Obsidian / WikiHub / Markdown tools
```

## Step 1 — Install Hermes Agent locally

For beginners on macOS or Windows, start with Hermes Desktop:

* Download: [Hermes Desktop](https://hermes-agent.nousresearch.com/desktop)

* Docs: [Hermes installation guide](https://hermes-agent.nousresearch.com/docs/getting-started/installation)

Hermes Desktop installs both the desktop app and the `hermes` command-line tool.

If you prefer command-line only on Linux, macOS, WSL2, or Termux:

```bash
curl -fsSL https://hermes-agent.nousresearch.com/install.sh | bash
```

Then run the simplest setup path:

```bash
hermes setup --portal
hermes doctor
```

`hermes setup --portal` is currently the fastest beginner path because one OAuth setup can configure a model provider plus built-in tool gateway features like web search, browser, image generation, and TTS.

## Step 2 — Optional remote/server setup in two steps

If you want your agent to run somewhere that is not your laptop, use either a normal remote server over SSH or a managed cloud workspace such as Daytona. If you have access to `cortex.ideaflow.app`, that can be a good free/low-friction place to start experimenting with a hosted workspace.

### Option A: install Hermes directly on the remote server

1. SSH into the server and install Hermes:

```bash
ssh ubuntu@your-server
curl -fsSL https://hermes-agent.nousresearch.com/install.sh | bash
hermes setup --portal
hermes doctor
```

1. Keep it reachable from your phone or desktop using the gateway when ready:

```bash
hermes gateway setup
hermes gateway run
```

Use this when you want Hermes itself to live on the server.

### Later: local Hermes + SSH remote backend

There is also a useful advanced setup where Hermes Desktop stays local, but terminal work executes on a remote server over SSH. We are leaving that out of the beginner path for now to keep the tutorial simple. Consider bringing it back later for users who already have a VPS and want local Desktop UX with remote execution.

### Option B: Daytona cloud workspace backend

Daytona is a managed cloud workspace backend. It is useful when you want persistent cloud sandboxes that can stop/resume instead of running all the time.

1. Add a Daytona API key and enable the backend:

```bash
hermes config set DAYTONA_API_KEY your_daytona_key_here
hermes config set terminal.backend daytona
hermes config set terminal.container_persistent true
```

1. Verify it:

```bash
hermes doctor
hermes chat -q "Create a hello.txt file, print pwd, and confirm this is running in Daytona" --toolsets terminal,file
```

Docs: [Hermes terminal backend configuration](https://hermes-agent.nousresearch.com/docs/user-guide/configuration).

## Step 3 — Create your personal LLM Wiki folder

An LLM Wiki is a Markdown knowledge base that the agent maintains over time. The important files are:

```text
wiki/
├── SCHEMA.md       # rules, domain, tags, page conventions
├── index.md        # map of every page and one-line summaries
├── log.md          # append-only history of wiki changes
├── raw/            # immutable source material
├── entities/       # people, orgs, products, projects
├── concepts/       # reusable ideas and topics
├── comparisons/    # side-by-side analyses
└── queries/        # useful answers worth saving
```

Create a folder:

```bash
mkdir -p ~/wiki/{raw/articles,raw/transcripts,raw/assets,entities,concepts,comparisons,queries}
```

Then ask Hermes:

```text
Create a new LLM Wiki in ~/wiki. The domain is my personal second brain: projects, people, meetings, IdeaFlow notes, useful decisions, and recurring workflows. Use the llm-wiki skill conventions. Create SCHEMA.md, index.md, and log.md.
```

The AGI House LLM Wiki is a useful example of the end state: [AGI House LLM Wiki](https://jacobcole.wikihub.md/@jacobcole/agi-house-llmwiki/index).

## Step 4 — Open the wiki in Markdown tools

Recommended tools:

* [Obsidian](https://obsidian.md/) — best for browsing, graph view, wikilinks, backlinks, and manual editing.

* [OpenMarkdownReader v1.0.15](https://github.com/tmad4000/OpenMarkdownReader/releases/tag/v1.0.15) — lightweight Markdown reading tool.

* [WikiHub](https://wikihub.md/) — useful for publishing selected pages privately or publicly.

In Obsidian:

1. Open `~/wiki` as a vault.
2. Keep `[[wikilinks]]` enabled.
3. Set attachments to `raw/assets/`.
4. Optional: install Dataview for frontmatter-powered tables.

## Step 5 — Tell Hermes where the wiki lives

Add the wiki path to Hermes’ environment:

```bash
hermes config set WIKI_PATH ~/wiki
hermes config set OBSIDIAN_VAULT_PATH ~/wiki
```

Then install or load the useful wiki skills:

```bash
hermes skills install llm-wiki
# When the IdeaFlow skill PR lands upstream, install it from the skills catalog.
# Until then, inspect/install from the public SKILL.md URL:
hermes skills inspect https://raw.githubusercontent.com/tmad4000/hermes-agent/feat/ideaflow-obsidian-llm-wiki/skills/research/ideaflow-obsidian-llm-wiki/SKILL.md
```

In a Hermes chat, you can also say:

```text
Use the llm-wiki skill. My wiki is at ~/wiki. First read SCHEMA.md, index.md, and the last 30 lines of log.md before making changes.
```

The most important maintenance skill is **`llm-wiki`**: it teaches Hermes to orient on `SCHEMA.md`, `index.md`, and `log.md`; ingest sources into `raw/`; update entity/concept pages; maintain wikilinks; and lint the wiki for broken links, missing frontmatter, stale pages, and orphan notes.

Use **`ideaflow-obsidian-llm-wiki`** when you want IdeaFlow / Thoughtstream to feed that same wiki through heartbeat-driven imports.

## Step 6 — Connect IdeaFlow / Thoughtstream heartbeat ideas

The IdeaFlow workflow is:

1. IdeaFlow captures live thoughts, tasks, tags, and meeting notes.
2. A heartbeat job checks for new or changed notes.
3. Hermes imports durable notes into `raw/ideaflow/` or `raw/transcripts/`.
4. Hermes updates the LLM Wiki pages, index, and log.
5. Obsidian / WikiHub become the readable surface for the compiled knowledge.

Use the skill:

* Public GitHub skill: [IdeaFlow → Obsidian LLM Wiki skill](https://github.com/tmad4000/hermes-agent/blob/feat/ideaflow-obsidian-llm-wiki/skills/research/ideaflow-obsidian-llm-wiki/SKILL.md)

* Private WikiHub mirror: [@jacobcole/ideaflow-obsidian-llm-wiki](https://wikihub.md/@jacobcole/ideaflow-obsidian-llm-wiki)

Example heartbeat prompt:

```text
Every heartbeat, check IdeaFlow for notes changed since the last run. If a note has #llmwiki, import it into my LLM Wiki. If a note has #live-meeting, append concise running bullets to the note and save durable decisions to raw/transcripts/. If a note has #defer1mo, turn it into a deferred follow-up task for one month from the note date. Always update index.md and log.md.
```

## Example heartbeat use cases from the Tejas / IdeaFlow meeting

Source note: Otter transcript titled **“AI Integration Workshop”** from the recent meeting set. The transcript discussed several concrete IdeaFlow + Hermes heartbeat ideas:

* **Read recent IdeaFlow notes:** ask Hermes to read a few recent notes from IdeaFlow, summarize them, and identify follow-ups.

* **Keyword-triggered agents:** if a note contains a certain keyword or tag, the heartbeat can invoke an agent action.

* **Inline agent responses:** a note can say `@agent research this`, `@agent file a bug report`, or `@agent enrich this`, and Hermes can respond by appending output back into the note or wiki.

* **Live meeting notes:** if a note has `#meeting` or `#live-meeting`, the heartbeat can append semi-real-time bullets like “key things to remember from this meeting.”

* **Faster heartbeat during live meetings:** once `#live-meeting` is detected, temporarily run the heartbeat more often so useful notes appear while the meeting is still happening.

* **Deferred tasks:** tags like `#defer1mo` can become future reminders or tasks, e.g. “cancel subscription one month from this note’s date.”

* **Cross-channel follow-ups:** Hermes can transform meeting or IdeaFlow notes into follow-ups for email, docs, GitHub issues, bug reports, or personal task lists.

A beginner-friendly tag taxonomy might be:

```text
#llmwiki       import this into the durable wiki
#meeting      summarize after the meeting
#live-meeting append running bullets during the meeting
#defer1mo     create a one-month deferred follow-up
#agent        explicit instruction for Hermes
#bug          file or draft a bug report
#research     do background research and add sources
#decision     preserve as a decision record
```

## Step 7 — First “agent with second brain” test

Try this end-to-end beginner test:

1. Create a note in IdeaFlow or Obsidian:

```markdown
# First second-brain test #llmwiki #agent

I want Hermes to remember that my second brain is a Markdown LLM Wiki in ~/wiki.
The wiki should track projects, meetings, people, ideas, and deferred follow-ups.

@agent Add this as a concept page and update the index/log.
```

1. Tell Hermes:

```text
Use the llm-wiki skill. Process my first second-brain test note into ~/wiki. Create or update the right concept page, add wikilinks, update index.md, and append log.md.
```

1. Open Obsidian and verify:

* A new concept/entity page exists.

* `index.md` links to it.

* `log.md` records the change.

* The page has at least two useful wikilinks or placeholders for related concepts.

## Step 8 — Keep it alive with scheduled maintenance

Once the basics work, schedule maintenance:

```text
Create a Hermes cron job that runs every day at 8am. It should use the llm-wiki skill, read ~/wiki/SCHEMA.md, ~/wiki/index.md, and the last 30 lines of ~/wiki/log.md, then report broken links, orphan pages, stale pages, and suggested next sources to ingest.
```

For IdeaFlow heartbeat sync, schedule a shorter interval only if the source is safe and rate limits are understood:

```text
Create a Hermes cron job every 30 minutes that uses ideaflow-obsidian-llm-wiki. It should check for changed IdeaFlow notes, import notes tagged #llmwiki or #meeting into ~/wiki, and append a concise summary of changes to log.md. Do not expose tokens or raw private notes outside the private wiki.
```

## Safety defaults

* Keep private notes private by default.

* Store API keys only in `~/.hermes/.env`, Keychain, or provider auth stores — never in wiki pages.

* Keep raw sources in `raw/` immutable; edits and synthesis go in entity/concept pages.

* Ask before publishing pages publicly.

* Use remote, Docker, SSH, Daytona, or Cortex-style sandboxes for risky code execution.

## The shortest possible recipe

```bash
# 1. Install Hermes
curl -fsSL https://hermes-agent.nousresearch.com/install.sh | bash
hermes setup --portal

# 2. Create wiki folder
mkdir -p ~/wiki/{raw/articles,raw/transcripts,raw/assets,entities,concepts,comparisons,queries}
hermes config set WIKI_PATH ~/wiki
hermes config set OBSIDIAN_VAULT_PATH ~/wiki

# 3. Ask Hermes to initialize it
hermes chat -q "Use llm-wiki. Create a personal second-brain LLM Wiki in ~/wiki for projects, meetings, people, IdeaFlow notes, and recurring workflows."

# 4. Open it
# Download Obsidian: https://obsidian.md/
```

That gives you a simple agent + second brain loop: capture in IdeaFlow, maintain with Hermes, browse in Obsidian, and publish selected knowledge through WikiHub.