How to Connect Obsidian + Hermes Agent Into One System That Thinks, Remembers, and Runs Your Life

Most productivity systems have a memory problem.

Your Obsidian vault stores everything you know but cannot act on it without you initiating something.

Your AI agent can act on anything but forgets everything the moment the session closes.

Connect them and the problem disappears entirely.

Obsidian becomes the permanent knowledge layer. Every note, every decision, every captured idea, every project update lives there as plain text that never disappears.

Hermes Agent becomes the intelligence layer that reads that knowledge, reasons across it, executes workflows against it, and writes new knowledge back into it automatically.

Together they form a system that thinks with your accumulated knowledge, remembers everything across every session, and runs your most important recurring workflows while you sleep.

This guide is the complete build.

Why This Combination Works

Before the architecture understand why these two tools belong together.

The problem with Obsidian alone:

Obsidian is the best knowledge storage system available. Plain text files. Local storage. Permanent. Searchable. Linkable. But Obsidian is passive. It stores what you put in and returns it when you search for it. It does not read your notes and surface insights. It does not run workflows. It does not generate outputs from your accumulated knowledge without you manually asking for them.

The problem with Hermes Agent alone:

Hermes is the best autonomous agent framework available. Persistent memory. Skill execution. Scheduled automation. MCP connections to real tools. But Hermes memory lives in a SQLite database. It is not human-readable. You cannot open it, browse it, or edit it directly. You cannot build a rich knowledge network inside it the way you can in Obsidian.

What the combination produces:

Obsidian handles human-readable permanent storage. You read it, write in it, link notes together, and build a knowledge network that compounds over years.

Hermes reads your Obsidian vault via the Filesystem MCP, reasons across everything in it using Claude, executes automated workflows that produce new knowledge, and writes the outputs back into your vault as new notes.

The vault is not just where you store things. It is the operating environment that Hermes runs against.

Every note you write becomes context Hermes uses.

Every output Hermes generates becomes a note you can read, edit, and link.

The two systems compound together rather than operating in parallel.

The Architecture

The system has four layers that work together.

Layer 1: The Vault Layer — Obsidian

Plain text Markdown files organized in a structure designed for both human navigation and automated processing. Every note you write, every idea you capture, every decision you make lives here.

Layer 2: The Connection Layer — Filesystem MCP

The bridge between Obsidian and Hermes. The Filesystem MCP gives Hermes direct read and write access to your Obsidian vault. Hermes can read any note, search across all notes, create new notes, and update existing ones.

Layer 3: The Intelligence Layer — Hermes + Claude

Hermes executes skill files that call Claude via the Anthropic API. Claude reads your vault, reasons across your accumulated knowledge, and produces outputs that go back into the vault as new notes.

Layer 4: The Automation Layer — Hermes Scheduler

Scheduled workflows that fire automatically at configured times. Morning briefings generated from your vault before you wake up. Weekly reviews synthesized every Sunday evening. Project status updates produced every Monday morning. All of it running without you initiating anything.

Setting Up the Connection

Step 1: Install Hermes Agent

git clone https://github.com/hermes-agent/hermes

cd hermes

npm install

Step 2: Configure Claude as the model

Open .env and configure:

MODEL_PROVIDER=anthropic

MODEL_NAME=claude-opus-4-8

ANTHROPIC_API_KEY=your-anthropic-api-key

MEMORY_BACKEND=sqlite

MEMORY_PATH=./data/memory.db

ENABLE_SCHEDULER=true

SCHEDULER_TIMEZONE=America/New_York

Step 3: Configure the Filesystem MCP to point at your Obsidian vault

MCP_FILESYSTEM_PATH=/Users/yourname/Documents/YourVaultName

This single configuration is what connects everything. Hermes now has direct access to every note in your vault.

Step 4: Install and configure the MCP server

npm install -g @modelcontextprotocol/server-filesystem

npm install -g @modelcontextprotocol/server-brave-search

Step 5: Start Hermes and verify the connection

npm run start

Test the connection:

List the top-level folders in my Obsidian vault

and describe the structure you see.

Hermes should accurately describe your vault's folder structure. The connection is live.

The Vault Structure for the Combined System

The vault structure needs to accommodate both human navigation and automated processing. Hermes needs to know where to read inputs and where to write outputs. You need to know where to find everything Hermes produces.

VAULT/

00 - INBOX/

[raw captures that need processing]

01 - NOTES/

permanent/

[atomic notes in your own words]

daily/

[YYYY-MM-DD].md

meetings/

[YYYY-MM-DD]-[meeting-name].md

02 - PROJECTS/

[project-name]/

overview.md

tasks.md

notes/

03 - RESOURCES/

[topic-based reference notes]

04 - HERMES-OUTPUTS/

briefings/

[YYYY-MM-DD]-morning-briefing.md

analyses/

[YYYY-MM-DD]-[topic]-analysis.md

syntheses/

[YYYY-MM-DD]-[topic]-synthesis.md

reviews/

[YYYY-MM-DD]-weekly-review.md

05 - ARCHIVE/

[completed projects and outdated material]

06 - SYSTEM/

CLAUDE.md

skills/

templates/

The HERMES-OUTPUTS folder is the critical addition. Every automated output Hermes generates lands here. You always know where to find what Hermes produced. You can read it, edit it, link it to other notes, and build on it.

The SYSTEM folder contains your CLAUDE.md and optionally copies of your Hermes skill files for reference. Keeping skill documentation in the vault means your notes about how the system works live alongside the knowledge the system produces.

The CLAUDE.md That Powers the System

The CLAUDE.md lives in your Obsidian vault at 06 - SYSTEM/CLAUDE.md. Hermes reads it via the Filesystem MCP at the start of every skill execution.

Obsidian + Hermes System — CLAUDE.md

Vault Location

This file is at: 06 - SYSTEM/CLAUDE.md

All outputs save to: 04 - HERMES-OUTPUTS/

Who I Am

Name: [YOUR NAME]

What I do: [YOUR PRIMARY WORK]

Primary focus: [YOUR MOST IMPORTANT AREA]

How My Vault Is Organized

00 - INBOX: Raw unprocessed captures

01 - NOTES: Processed permanent notes and daily notes

02 - PROJECTS: Active project folders

03 - RESOURCES: Reference material by topic

04 - HERMES-OUTPUTS: All automated outputs

05 - ARCHIVE: Completed and outdated material

06 - SYSTEM: CLAUDE.md and system files

Active Projects

[PROJECT 1]: [ONE SENTENCE STATUS]

Next action: [SPECIFIC NEXT STEP]

[PROJECT 2]: [ONE SENTENCE STATUS]

Next action: [SPECIFIC NEXT STEP]

Current Priorities

1. [MOST IMPORTANT THING THIS WEEK]
2. [SECOND MOST IMPORTANT]
3. [THIRD MOST IMPORTANT]

Topics I Think About Most

[LIST 5-8 RECURRING TOPICS]

Writing Voice

[HOW YOU WRITE AND COMMUNICATE]

[Specific things you never say or do]

Output Instructions

When generating any output:

• Read the relevant section of my vault first
• Reference specific notes by their file path
• Save outputs to the correct subfolder in 04 - HERMES-OUTPUTS
• Date-stamp every file: YYYY-MM-DD-[type]-[topic].md
• Create proper Obsidian frontmatter with type and date

Memory Instructions

Before any skill execution:

• Read relevant memory from Hermes database
• Read relevant notes from vault via Filesystem MCP
• Combine both sources for full context

After any skill execution:

• Store summary in Hermes memory with appropriate tags
• Create or update the relevant vault note

Weekly Update

This file is reviewed and updated every Monday.

Current week priorities updated: [DATE]

The Seven Skills That Make the System Work

Skill 1: The Vault-Aware Morning Brief

This skill reads your actual Obsidian vault to generate a morning brief that is specific to your projects, your notes, and your current priorities rather than generic news.

Create skills/vault-morning-brief.md:

vault-morning-brief

Purpose

Generate a morning brief using my actual Obsidian

vault as the primary context, supplemented by

real-time web search for external developments.

Trigger

Scheduled daily at 6:00 AM.

Manual: "Generate my morning brief"

Process

1. Read CLAUDE.md from my vault at 06 - SYSTEM/CLAUDE.md

1. Read today's daily note if it exists at 01 - NOTES/daily/[TODAY'S DATE].md

1. Read all project overview.md files in 02 - PROJECTS/ to understand current project status

1. For each active project in CLAUDE.md: Check if any tasks are overdue by reading the project's tasks.md file

1. Read the most recent weekly review from 04 - HERMES-OUTPUTS/reviews/ to understand last week's priorities and outcomes

1. Use Brave Search to find external developments relevant to my current priorities from CLAUDE.md

1. Synthesize everything into the morning brief:

Morning Brief — [DATE]

MOST IMPORTANT TODAY

[Single highest-leverage action based on

vault context and current priorities]

PROJECT PULSE

For each active project:

[PROJECT NAME]: [One sentence status]

Next: [Specific next action from tasks.md]

OPEN LOOPS

[Any items from yesterday's daily note

or recent notes marked as unfinished]

EXTERNAL SIGNAL

[1-3 external developments relevant to

my current priorities]

FROM MY VAULT

[One connection between something in my

notes and something happening today]

1. Save to: 04 - HERMES-OUTPUTS/briefings/[DATE]-morning-brief.md

1. Create today's daily note at 01 - NOTES/daily/[DATE].md if it does not exist, with a link to the morning brief

Output Format

The brief should reference specific note paths

in my vault. Not generic observations.

Specific connections to actual notes I have written.

Skill 2: The Inbox Processor

This skill empties your INBOX folder every evening, filing notes into the correct location and creating links to related permanent notes.

Create skills/inbox-processor.md:

inbox-processor

Purpose

Process all files in 00 - INBOX, file them

in the correct vault location, and create

connections to related existing notes.

Trigger

Scheduled daily at 8:00 PM.

Manual: "Process my inbox"

Process

1. Read CLAUDE.md for vault structure and context.

1. List all files currently in 00 - INBOX

1. For each file in INBOX:

a. READ the file content fully

b. CLASSIFY the note type:

• PERMANENT IDEA: deserves its own atomic note
• PROJECT NOTE: belongs in a specific project
• REFERENCE: belongs in 03 - RESOURCES
• DAILY CAPTURE: belongs in today's daily note
• TASK: belongs in a project's tasks.md

c. FIND CONNECTIONS: Search the vault for

existing notes that relate to this capture.

Look in 01 - NOTES/permanent/ primarily.

d. PROCESS the note:

For PERMANENT IDEA:

Create a new note at

01 - NOTES/permanent/[concept-name].md

with proper frontmatter and links to

related notes found in step c.

For PROJECT NOTE:

Append to the relevant project's notes

or create a new note in

02 - PROJECTS/[project-name]/notes/

For REFERENCE:

Create or append to the relevant topic

file in 03 - RESOURCES/

For DAILY CAPTURE:

Append to 01 - NOTES/daily/[TODAY].md

For TASK:

Append to the relevant project's tasks.md

e. ARCHIVE the original inbox file to

05 - ARCHIVE/inbox-processed/

1. Generate a processing summary: [N] notes processed [N] permanent notes created [N] project notes filed [N] connections made

1. Save summary to: 04 - HERMES-OUTPUTS/[DATE]-inbox-summary.md

Quality Standard

Every permanent note created should have

at least one link to an existing note.

A permanent note with no connections is

not ready for the permanent folder.

Skill 3: The Project Health Monitor

This skill reads every active project folder in your vault and produces a health assessment every Monday morning.

Create skills/project-health.md:

project-health

Purpose

Read all active project folders and produce

a comprehensive project health report.

Trigger

Scheduled every Monday at 7:00 AM.

Manual: "Check project health"

Process

1. Read CLAUDE.md for list of active projects.

1. For each active project in 02 - PROJECTS/:

a. Read overview.md

b. Read tasks.md

c. Read all notes in the project's notes/ folder

d. Check date of last modification on any file

in the project folder

1. For each project Claude assesses:

STATUS: On Track / At Risk / Stalled / Blocked

EVIDENCE: What specifically in the project files

indicates this status. Reference actual file content.

NEXT ACTION: Single most important thing this

project needs in the next 48 hours.

STALL FLAG: If no file in the project folder

has been modified in 7 or more days flag as stalled.

1. Generate the health report:

Project Health Report — [DATE]

Summary

[N] active projects: [N] on track, [N] at risk, [N] stalled

Project Status

[PROJECT NAME]

Status: [STATUS]

Evidence: [SPECIFIC REFERENCE TO VAULT CONTENT]

Next action: [SPECIFIC ACTION]

[Repeat for each project]

Attention Required

[Any project flagged as stalled or blocked

with specific recommendation]

1. Save to: 04 - HERMES-OUTPUTS/reviews/[DATE]-project-health.md

1. For any stalled project: add a REVIEW NEEDED note to the project's overview.md with today's date

Note

Reference specific file paths and note content

in the assessment. Generic observations about

project status are not useful. The report should

only say things that can be traced to specific

notes in the vault.

Skill 4: The Note Connection Finder

Once per week this skill reads all notes created or modified in the past seven days and finds connections to older notes that were not made at creation time.

Create skills/connection-finder.md:

connection-finder

Purpose

Find connections between recent notes and

older permanent notes that were not explicitly

linked at creation time.

Trigger

Scheduled every Sunday at 5:00 PM.

Manual: "Find note connections"

Process

1. List all files in 01 - NOTES/ modified in the past 7 days.

1. For each recently modified note:

a. Read the full note content

b. Search all permanent notes in

01 - NOTES/permanent/ for semantic

connections to this note's content

c. Identify connections that are NOT

already present as wikilinks in the note

d. For each new connection found:

• Name both notes
• Describe specifically how they connect
• Assess connection strength: Strong / Moderate / Weak
• Suggest the link text to use

1. Filter to only Strong and Moderate connections.

1. Generate the connection report:

Connection Report — [DATE]

New Connections Found

[N] connections across [N] notes

[NOTE NAME]

Path: [FILE PATH]

Connects to: [[OTHER NOTE NAME]]

Reason: [SPECIFIC DESCRIPTION OF CONNECTION]

Suggested link text: [HOW TO PHRASE THE LINK]

[Repeat for each connection]

Recommended Actions

Add these links this week to strengthen

the knowledge network.

1. Save to: 04 - HERMES-OUTPUTS/analyses/[DATE]-connections.md

Quality Standard

Only surface non-obvious connections. If the

link is already present or the connection is

trivially obvious from the note titles skip it.

The value is in finding the connections a human

reader would miss.

Skill 5: The Weekly Vault Synthesis

Every Sunday evening this skill reads your entire week of activity in the vault and produces a synthesis that reveals insights visible only across seven days of accumulated notes.

Create skills/weekly-synthesis.md:

weekly-synthesis

Purpose

Synthesize the full week's vault activity

into a comprehensive review that surfaces

patterns invisible in any individual day.

Trigger

Scheduled every Sunday at 7:00 PM.

Manual: "Generate weekly synthesis"

Process

1. Read CLAUDE.md for current priorities and active projects.

1. Read all daily notes from the past 7 days in 01 - NOTES/daily/

1. Read all permanent notes created or modified this week in 01 - NOTES/permanent/

1. Read all Hermes outputs from this week in 04 - HERMES-OUTPUTS/

1. Read the project health report from Monday in 04 - HERMES-OUTPUTS/reviews/

1. Claude synthesizes across all of it:

Weekly Synthesis — [WEEK OF DATE]

THE WEEK IN ONE LINE

[Single sentence capturing the most

important thing this week revealed]

WHAT MOVED FORWARD

[Specific progress on active projects

with references to vault evidence]

WHAT DID NOT MOVE

[Honest assessment of stalled items

and the most likely reason]

IDEAS THAT EMERGED

[New permanent notes created this week

that deserve attention]

THE PATTERN

[One theme that appeared repeatedly

across the week's notes]

CONNECTIONS MADE

[Most significant connections found

between notes this week]

NEXT WEEK PRIORITIES

[Three specific priorities for next week

ranked by impact, each with a next action]

CLAUDE.MD UPDATE NEEDED

[Any priority or project status changes

that should be reflected in CLAUDE.md]

1. Save to: 04 - HERMES-OUTPUTS/reviews/[DATE]-weekly-synthesis.md

1. Update CLAUDE.md Current Priorities section with next week's top 3.

Note

The synthesis should be the document you read

on Monday morning before anything else.

It should orient you to the week ahead using

the full context of the week that just ended.

Skill 6: The Research-to-Notes Converter

When you drop research material into INBOX, this skill converts it into properly structured permanent notes with connections to your existing knowledge.

Create skills/research-converter.md:

research-converter

Purpose

Convert research material dropped in INBOX

into properly structured permanent notes

connected to existing vault knowledge.

Trigger

Manual: "Convert research in inbox" or

"Process research on [TOPIC]"

Process

1. Read CLAUDE.md for vault context and current priorities.

1. Identify research material in 00 - INBOX by reading file contents and looking for source URLs, article text, or research notes.

1. For each research item:

a. READ the full content

b. EXTRACT the key ideas:

• What is the core claim?
• What is the supporting evidence?
• What is genuinely new versus what I likely already know?

c. SEARCH my existing vault for

01 - NOTES/permanent/ notes on related topics

d. CREATE a literature note at:

01 - NOTES/permanent/lit-[source-topic].md

Literature note format:

type: literature

source: [SOURCE NAME]

date_read: [TODAY]

topic: [TOPIC]

[SOURCE TITLE]

Core Argument

[What this source claims in my own words]

Key Evidence

[Specific evidence worth remembering]

My Reaction

[What I agree with, doubt, or want to explore]

Connections

[[RELATED PERMANENT NOTE 1]]

[[RELATED PERMANENT NOTE 2]]

Ideas to Develop

[Specific ideas worth turning into

their own permanent notes]

e. For each idea flagged in Ideas to Develop:

Create a new permanent note at

01 - NOTES/permanent/[concept-name].md

f. Move original inbox item to archive

1. Generate conversion summary: [N] literature notes created [N] permanent notes created [N] connections to existing notes

1. Save summary to: 04 - HERMES-OUTPUTS/analyses/[DATE]-research-converted.md

Quality Standard

Every literature note must produce at least

one new permanent note. If the research

produced no new ideas worth capturing as

permanent notes the research was not worth

processing in the first place.

Skill 7: The Thinking Partner

This skill activates Claude as an active thinking partner that reads your recent notes and asks questions, surfaces contradictions, and pushes your thinking forward.

Create skills/thinking-partner.md:

thinking-partner

Purpose

Activate Claude as an active thinking partner

that reads my recent vault activity and

engages with my ideas rather than just

storing or summarizing them.

Trigger

Manual: "Thinking partner session" or

"Challenge my thinking on [TOPIC]"

Process

1. Read CLAUDE.md for current intellectual context.

1. Read all permanent notes modified in the past 14 days.

1. Read recent daily notes from the past 7 days.

1. Claude identifies:

INTERESTING TENSIONS:

Notes where I appear to hold positions

that are in tension with each other.

Not contradictions necessarily.

Tensions worth examining.

UNDERDEVELOPED IDEAS:

Permanent notes that make a claim without

fully developing the reasoning or evidence.

MISSING CONNECTIONS:

Ideas in recent notes that connect to

older permanent notes in non-obvious ways.

OPEN QUESTIONS:

Questions raised in recent notes that

have not been answered anywhere in the vault.

1. Claude engages with each finding: Not just naming them. Pushing on them.

For TENSIONS: "You wrote X in [NOTE A]

and Y in [NOTE B]. These seem to pull

in different directions. Which position

do you actually hold and why?"

For UNDERDEVELOPED IDEAS: "The note on

[TOPIC] makes the claim that [CLAIM].

What is the strongest argument against

this? Does your vault contain evidence

that challenges it?"

For OPEN QUESTIONS: "You asked [QUESTION]

in your note from [DATE]. You have not

answered it anywhere. Is this worth

investigating or has it become irrelevant?"

1. Save the session to: 04 - HERMES-OUTPUTS/analyses/[DATE]-thinking-partner.md

Tone

This skill should feel like talking to a

smart colleague who has read everything in

your vault and is genuinely engaging with

your ideas. Not validating. Not summarizing.

Pushing. Questioning. Connecting.

The Daily Experience

With the full system running the daily experience of your Obsidian vault changes completely.

6:00 AM: Hermes reads your vault and generates the morning brief. You wake up to a note in HERMES-OUTPUTS/briefings/ that knows your project status, your open loops, your current priorities, and the external developments relevant to your work. Five minutes to read. You know exactly what matters before you see a single notification.

During the day: You capture everything to 00 - INBOX. Ideas, tasks, references, meeting notes. No filing decisions. No thinking about where things go. Just capture.

8:00 PM: Hermes processes your inbox automatically. Every capture gets filed, linked, and connected to your existing knowledge. Your INBOX empties itself. Nothing sits unprocessed.

Monday 7:00 AM: Project health report waiting in HERMES-OUTPUTS/reviews. Every active project assessed. Stalled projects flagged. Next actions surfaced. Your week starts with a complete picture of where everything stands.

Sunday 5:00 PM: Connection report lands in HERMES-OUTPUTS. Links between recent notes and older permanent notes that you did not consciously make surface automatically. Your knowledge network gets denser every week without additional effort.

Sunday 7:00 PM: Weekly synthesis ready. The full week's vault activity synthesized into a document that shows what moved, what did not, what patterns emerged, and what next week's priorities should be. Your CLAUDE.md updates automatically with next week's top three priorities.

What Happens After 90 Days

The power of this combination is not visible on day one.

It becomes visible over time as two separate compounding effects interact.

Obsidian compounds because your permanent notes accumulate connections over months. A note written in January gets linked to notes written in March, April, and May. The network gets denser. The connection finder surfaces increasingly non-obvious relationships. The vault at month three is qualitatively richer than the vault at month one.

Hermes compounds because memory accumulates across every session. The morning brief at day ninety has read three months of your daily notes and knows your patterns. The weekly synthesis at week twelve has twelve weeks of previous syntheses to draw on. The project health monitor at month three knows how your projects typically stall and surfaces that pattern before it becomes a problem.

The interaction compounds because the more Obsidian knows the better Hermes can reason. The more Hermes produces the richer the vault becomes. The richer the vault the better the next Hermes output.

By month three you have a system that no longer feels like a tool you use.

It feels like a thinking partner who has been working alongside you for months, knows everything you have written, and surfaces the connections and insights your own working memory cannot hold.

That is the system this combination is capable of producing.

Build it this weekend.

The compounding starts from the first skill that reads your vault.

Follow @cyrilXBT for every Obsidian system, Hermes Agent skill, and autonomous operation architecture that makes this combination run at its highest level.