Ben AI shows how to build a second brain in Obsidian that gives Claude Cowork, Claude Code, and other AI agents persistent business context, memory, and shared team knowledge.
Key Takeaways
- Persistent, structured context is the missing layer that lets AI agents function as a primary work interface.
- A local Obsidian vault connected to an AI agent eliminates repetitive re-explaining and enables consistent, personalized outputs.
- Bidirectional updates let the knowledge base grow automatically as teams use AI, compounding its value over time.
- Skills become lighter and faster to build when they reference a central second brain rather than bundling their own context files.
- Sharing one vault across a team gives all agents the same strategy and brand context, boosting productivity and alignment.
What the video covers
- AI agents like Claude Code, Claude Cowork, and Codex are improving at reasoning and coding, but lack persistent context about the user and their business.
- The speaker builds a 'second brain' in Obsidian containing context on his business, strategy, projects, brand, workflows, team, meetings, and himself, visualized as a linked graph.
- Because the agent can access this knowledge vault, users no longer need to re-explain their situation in every new chat; the agent pulls relevant context to answer questions like 'What should I focus on today?'
- Agents can write back to the second brain, so decisions and rules (e.g., avoiding em dashes in writing) stated in chats are saved and reused, improving outputs over time.
- Skills (saved step-by-step instructions for agents, such as a LinkedIn post writer) can point to shared context in the second brain instead of duplicating reference files, making skill-building faster and more consistent.
- The setup scales to teams: a shared vault with strategy, ICP, tone-of-voice references, and goals gives every team member's agent the same up-to-date context.
- Obsidian keeps everything local, avoiding the need for syncing services, APIs, MCP servers, or cloud software, and the tool is free.
- The speaker demonstrates a Claude.md instruction file that tells the agent how to navigate the vault, and provides starter folder structures, including a simplified personal OS version.
- Compounding advantage: the longer the vault is built and used, the more valuable it becomes, so late adopters fall behind on accumulated context.
- Recommended approach is to use Claude Cowork or Claude Code to help create and populate the initial vault structure.
Chapters
- 00:00Introduction: The Missing Context Layer for AI Agents
- 01:32Advantage 1: Persistent Context Across Chats
- 03:04Advantage 2: Agents Updating the Second Brain
- 04:35Advantage 3: Building Better and Faster Skills
- 06:35How It Works: Local Obsidian Setup and Claude.md
- 10:10Setting Up Your Vault Structure and Starter Templates
- 13:20Personal OS Example and Getting Started
Full Transcript — Download SRT & Markdown
Speaker A
Every month, AI agents on Claude Code, Claude Cowork, and Codex are getting better at reasoning, writing code, and navigating software. But for AI agents to actually become our main interface for work and doing work autonomously, there's still one missing layer: context.
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context. So in this video, I'll show you how I built a second brain in Obsidian that plugs into Co-work, CloudCode, or any AI agent I use, giving them persistent context and memory around me and my business. I'll cover the five big
Speaker A
So in this video, I'll show you how I built a second brain in Obsidian that plugs into Claude Cowork, Claude Code, or any AI agent I use, giving them persistent context and memory around me and my business. I'll cover the five big advantages of this setup and show you why this might have huge implications for how we work and how businesses are run. I'll also show you how it actually works and an easy way for you to set it up and get started with this today.
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before showing you how this works, how to set it up, and why I recommend starting with this today, let me quickly go over the five big advantages with some examples of having a second brain.
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Now, before showing you how this works, how to set it up, and why I recommend starting with this today, let me quickly go over the five big advantages with some examples of having a second brain.
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agent has persistent access to all of this context. And not just a few facts, but detailed context around everything.
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The first one is the most obvious, and it's persistent context. Right now, most people use AI in isolated conversations. You have to re-explain everything in each chat about your situation, your project, your workflows, and so on. With a second brain, your AI agent has persistent access to all of this context, and not just a few facts, but detailed context around everything.
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of these documents. For example, my AI accelerator here and here's me. Now I'll show you later how this actually works and how to set this up, but because of this, I can now open a new chat session with, for example, Cloud Co-work and ask
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You can see in my Obsidian that I have context saved around everything: my business, my strategy, my projects, my brand, my workflows, my team, myself, my meetings, literally everything. Here in this graph view, we can see the relationships between all of these documents. For example, my AI accelerator is here, and here's me. I'll show you later how this actually works and how to set it up, but because of this, I can now open a new chat session with, for example, Claude Cowork and ask something like, "What should I focus on today?" It's already connected to my knowledge vault, as Obsidian calls it. You can see Claude now pulls my context to give me an answer. Because it pulled this context, it knows that my main priorities should be landing page copy changes, recording the Obsidian video, and organizing the Spain offsite in April.
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my main priority should be landing page copy changes, recording the Obsidian video, and organizing the Spain offsite in April. I could even ask it things like, "Write me a LinkedIn post based on AI topics we discussed in our team
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I could even ask it things like, "Write me a LinkedIn post based on the AI topics we discussed in our team meetings this week, using the LinkedIn instant skill." It will go through our team meetings, see what AI topics we discussed, use a LinkedIn skill to write the post in my tone of voice, pull the context from my second brain, and output a LinkedIn post on the topic we discussed, which of course is this second brain topic. This week, my team and I built something different. We created a second brain for our entire business. This is just one example, but you can see the power of it. And with the new scheduled task feature, this becomes even more powerful.
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Then pulls the context from my second brain, uses the skill, and then output a LinkedIn post according to the topic we discussed, which is of course this second brain topic. This week, my team and I built something different. We
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Second, besides Cowork always being able to pull up-to-date and complete context around me and my business in any chat, it can also directly update the context in my second brain. Any decision, rule, or project update I make in an AI chat can be logged directly back into my second brain. For example, if I see something in this LinkedIn skill that I don't like, such as never using em dashes when writing content for me, I can say, "Remember this in my second brain or in my AI operating system." You can see it now saved and updated in my second brain as a rule in the writing preferences. This is huge, because it means the more you and your team use AI to do tasks, the more context is built, the more guidelines it has, and the better your AI becomes for yourself and your entire team.
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Secondly, besides co-work now always being able to pull up-to-date and complete context around me and my business in any chat, it can also directly update the context in my second brain. So, any decision, any rule, any project update I make in an AI chat, it
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Third, there's also a big advantage of having this second brain when building and using skills. If you don't know what skills are yet, they're basically saved instructions for your AI agent on Claude Code or Claude Cowork, explaining how to carry out a specific process or task. For example, this LinkedIn skill goes through the step-by-step process of writing a LinkedIn post in my style, and essentially allows these agents to automate workflows, just like in the example I showed you. I'll link a full video covering skills in the description below if you're still unfamiliar with them. But what changes with this second brain?
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in my second brain or in my AI operating system." You can see it now saved and updated this in my second brain as a rule in the writing preferences. Now, this is huge because it means the more you and your team use AI to do tasks,
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Skills usually have reference files and context inside the skill folder. For example, this LinkedIn skill has a pen profile background document, a hook template document, an ICP document, a LinkedIn example document, and a voice personality document. We use these reference files to get better outputs, but it usually takes a long time to provide all the context every new skill needs to produce good output. If you already have all of the relevant context around your ICP, your tone of voice, and your business in your second brain, you can build good skills far faster.
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you don't know what skills are yet, skills are basically saved instructions for your AI agent on Cloud Code or Cloud Co-work on how to do a specific process or task. For example, in this LinkedIn skill, it goes through the step-by-step
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This means you only need to lay out the process and point the skill to the right context in your second brain, rather than giving it the same context over and over for each new skill. For example, I have dozens of skills that share reference files about my ICP, their pain points, what my business does, and so on. As you can see, my newsletter writer skill shares many of the same context files as my LinkedIn one. So the new way I'm building skills with this second brain setup is not by adding extra context or reference files to the skill itself, but by pointing the skill to the right context in my second brain. For example, this is my new LinkedIn skill, the LinkedIn Instant. Here you can see that I only have the SKILL.md file with the process instructions, and in it I direct the skill to where it can find the specific context files in my second brain.
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I'll make sure to link in the description below, too. But what changes with this second brain? Skills usually have reference files and context inside the skill folder. For example, in this LinkedIn skill, I have a pen profile background document, a hook template
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This means any update I make to a reference file in my second brain, such as the ICP document, instantly updates every skill that uses it, instead of me manually updating dozens of skills myself. It also means the rule I added, "Never use em dashes when writing content for me," is now stored in my writing preferences, which is one of the documents many of my content-writing skills point to. So my newsletter skill is automatically updated with the same rule.
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a good output. And if you have all of the relevant context around your ICP, your tone of voice, your business already in your second brain, it means you can build good skills far faster.
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Another huge advantage of this setup is that it works across any AI you use. Your second brain in Obsidian is really just a folder of markdown files, which I'll explain in more detail in a moment. I can give Claude Cowork access to that folder, give Claude Code access, give Codex, or give any other AI agent provider access. For example, I can go to the Code tab, or just use Claude Code in the terminal, give it access to the same folder, the Ben AI OS, and ask the same question, "What should I focus on today?" As you can see, Claude Code has access to the same context and returns landing page copy, the Obsidian video, and the Spain offsite. This even works across different AI providers. Here I gave Codex access to the same folder and asked it the same question, and it returned landing page copy, YouTube production, and the Spain offsite.
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have dozens of skills that share reference files around my ICP, their pain points, what my business does, et cetera. As you can see, my newsletter writer skill shares a lot of the same context files as my LinkedIn one. So,
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Lastly, which is huge if you run a business, this isn't only for yourself. It can scale across your entire team. My team and I now share this same second brain, with our business strategy, our ICP understanding, our tone of voice references, our company goals, and more. Instantly, my entire team's AI agents have access to this context, which makes them far more powerful and productive for our business. For example, my entire team always has access to up-to-date strategy documents and ICP documents that their agents can use immediately.
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my new LinkedIn skill, the LinkedIn Instant, and in this case, you can see that I only have the skill MD, only the process instructions, and there I direct it to where I can find the specific context files in my second brain. And
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this means that any update I make to a reference file in my second brain, for example, in the ICP document, all of the skills that use this ICP document are instantly updated instead of me manually updating dozens of skills myself. It
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also means that this rule, for example, that I added, "Never use M dashes when writing content for me," is now updated as a rule in my writing preferences, which is one of the documents many of my content writing skills point towards.
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So, my newsletter skill is automatically updated with this same rule. Now, another huge advantage of this setup, of course, is that it works across any AI you use. So, your second brain in Obsidian is really just a folder of
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markdown files, which I'll explain in more detail in a second, but that's all it is. It's just a folder that I can now give Cloud Co-work access to, I can give Cloud Code access to, I can give Code X,
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Integra BT, or any other AI agent provider access to. For example, I can go to the code tab or just use Claude Code in the terminal, give it access to the same folder of my second brain, the Ben AI OS, and I can ask the same
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question, "What should I focus on today?" And as you can see, Claude Code has access to the same context. As you can see, landing page copy, Obsidian video, and Spain offsite. And this even works across different AI providers. Here I
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gave Code X access to the same folder, asked it the same question. As you can see, landing page copy, YouTube production, and Spain offsite. And then lastly, which is huge if you're a business, is that this is not only for
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yourself, but can actually scale across your entire team and business. Me and my team now share this same second brain with my business strategy, ICP understanding, uh tone of voice references, company goals, etc. So, instantly my entire team's AI agents
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have access to this context that make them far more powerful and productive for my business. For example, my entire team will always have access to up-to-date strategy documents, ICP documents that their agents can instantly use. And with the context and
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skills that I've built, I can now let an engineer write my LinkedIn post with an on-point tone of voice. In Obsidian, I can sync these updates in my context across the entire team here. And you can imagine that this setup could completely
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change the way you run a business, which I'll get to later in this video. But let me first explain how this actually works, because it might look a little bit overwhelming and complicated, but it really is not. So, what is Obsidian? All
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Obsidian really is is just a visual overlay over a folder and its files on your computer.
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As you can see here, all these folders that I'm seeing in Obsidian, context, daily departments intelligence onboarding, I also have available here in the folder that Obsidian is connected to.
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And all we really do is we point Claude Co-work, Claude Code, or Code X, or any other AI agent we use to the same folder on your computer, so they can directly read and write to the same files you see
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in Obsidian. And that's why Obsidian is a great app to do this on, because we don't have to sync anything, use an API or an MCP or a cloud-based software, it's all local. So, in Co-work, for example, all I do is give it access to
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that folder. But if we have thousands of these context files, how does our AI agent on Claude Co-work or Claude Code actually know what context to use? And how does it update it? Now, again, this is pretty simple. The way it updates and retrieves
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the right data from your Obsidian folder or vault is through the Claude bot MD file. Now, the Claude MD file is basically just an instruction you give to your AI agent on Claude Co-work or Claude Code on how to navigate the
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second brain or the folder. So, if I ask Co-work a question like, "What did we talk about in our team meeting yesterday?" my AI agent, first of all, knows that it needs more context to answer this question. It then reads the
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Claude MD file to understand where in my Obsidian vault or folder it will find more information around this. Then it reads those specific documents, like for example, yesterday's Fireflies transcript, to answer the question back to the user. You can basically see that
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Claude MD file as sort of like a system prompt or an instruction layer that tells your AI agent how the vault or your folder is structured and where to retrieve and save data. So, as you can see in this session with Claude Co-work
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where we wrote the LinkedIn post, it has access to one file, which is the instructions or the Claude MD, and this is basically just instructions for the AI agent on where to find specific information in the second brain and
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where to save it. You can see how the system works, the file structure, knowledge routing, and this same Claude MD file or the instructions you also see here in the Obsidian vault. Now, don't worry, I'll show you later in this video
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exactly how to get to this Claude MD and how to set up these instructions easily.
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Now, you might be asking, "How's this actually different from Claude's built-in memory, and why would we actually need Obsidian if it's just a folder?" Now, first of all, Claude's built-in memory is very limited and is basically designed to remember the most
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of essential facts about you. It's generally stored in one document, so the difference really is the scope of the context. My Obsidian vault, as you can see, has thousands of pieces of context.
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And secondly, if Obsidian is just a folder, why would we need Obsidian? The short answer is you don't need it. You can set this up in a folder yourself, too, but honestly, it's just a nice way for you to visualize, organize,
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navigate, search, and link your notes and files together. My context and knowledge sources over the last weeks have been growing really fast, and honestly, without Obsidian, I wouldn't be able to organize it the way that I have right now. Through the graph view,
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we can also see the relationships between all of these context files. It automatically makes these connections between different documents or context files. For example, in the brand identity document, you can see that we have the voice positioning, where it
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links to the ICP for our ideal customer profile and the pain points of our customer. This is also what your AI agent is able to navigate. So, for example, if it reads the brand guidelines and feels like it needs more
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context around my ICP, you can see this link or wiki link, what they call it, and actually look up this document to find more information. And the nice thing about Obsidian is I can really easily sync the updated context across
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my team if you're going to use this in a team setting. It's also entirely free to use and download, so I just recommend using it. Now, before showing you how to set it up, let me zoom out for 1 second
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because I think this setup has much bigger implications than just some extra productivity. I think it could entirely change the way people work and businesses are run. So, there are multiple of these big developments coming together right now in AI.
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Everyone can see that these LLMs are becoming better at reasoning, MCPs are getting better and now allow them to efficiently navigate softwares and the internet, and skills, plugins, schedule tasks, etc. now allow you to automate repetitive tasks fast and easily. But
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the missing layer for those AI agents was really context. And with a setup like this, I think it will slowly allow people and businesses to start adopting an AI interface like Cloud Co-work or Cloud Code as the main interface to do
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their work instead of hopping between 15 different softwares all the time. But maybe more importantly, I think this is the development that will slowly allow AI agents to start doing work autonomously without our involvement.
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Personally, for example, since I've really started using Co-work on a daily basis, I've been less and less in my Gmail inbox, I've been less on Google doing research, I'm barely in my CRM anymore, and now with this combination
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of MCPs, connectors, and scheduled skills, I can now automate end-to-end processes like email follow-ups without my involvement. And that's why I really believe you need to start building this today because the value of this setup isn't in the setup itself, it's in the
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context that builds over time. Every decision that gets logged, every correction or rule that gets saved, every project that gets documented, and every skill that gets made, it all compounds. So, the AI agent you and your entire team have after 6 months of using
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this is far more powerful than the one you start with on day one. And if your competitor, for example, starts 6 months after you, they're not just behind on the tool, they're behind on 6 months of intelligence that makes the tool
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actually perform far better for you. And even when better models come out and they will, the same context just becomes more powerful. So, the context, I think, will be your actual moat in the upcoming months and years. So, how do you
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actually set this up for yourself or your business? Now, the key thing to keep in mind when you get started is that you don't want to over-optimize. It might look very overwhelming what I just showed you in my own setup, but this
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setup I started with just probably five files a few weeks ago. This context will grow very naturally the more you use AI.
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You just want to sort of start very simple and let the system evolve naturally. The same is the case for the file structure. It is important, but you do want to start simple and let it evolve naturally. There is really no
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perfect file structure because it's going to be highly context-dependent. It will depend on your context, your business, your goals, and your projects.
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Um now, that being said, there are two file structures that I recommend and I've seen work well as a starting file structure. One for if you're running a business uh and you want to use this across your team, and one if you uh want
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to use this for yourself as a professional or as a solopreneur. Now, go over the file structure quickly so you understand what's in each because it is important, but we've also built a plugin you can use in your AI agent on
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Cloud Co-worker Cloud Code to help you set up and get to these starting structures fast, which I'll show you in a second how to use. A second what you want to keep in mind when I'm going through this is that many of these files
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are and can be created by your AI agent. So, don't get overwhelmed. You'll get there naturally. So, I'll cover the file structure that I use for my business setup and then I'll show you quickly the personal setup, which is basically the
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same but with less files. So, first we have the context folder and this is where you store general context around who you are, your business, your strategy, your team, your brand, and it's basically everything your AI agent needs to understand about you and your
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situation always. For example, in context I have information about my team strategy stakeholders pain points, organization, operator, the ICP, and the brand. Second, we have daily and this is basically where your AI agent logs everything that happened each day
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across your sessions, maybe across your meetings, and this is probably the most important one because it gives your AI agent that continuity between conversations. Then third, we have departments. Now, this is if you run a business, you will of course have
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different departments. For example, in my case, community, content, engineering partnerships operations et cetera. And then in the community folder, for example, we can have SOPs around work that needs to be done in my community, for example here, YouTube to
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community repurposing. The fourth one is intelligence and this is a bit like the first one, context, but much more detailed. And this is the place where things like meeting transcripts, decisions, competitor research, marketing sites get stored over time.
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Then we have onboarding. Here you can have SOPs around onboarding new team members or even clients. Then we have projects here. Now, projects will highly depend on your context. For me, projects can be, for example, different YouTube videos I'm working on
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so I can ideate and work on scripting on one video between different chats. If you run an agency, this can be a project for each client you're managing, but this will be highly context-dependent.
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Then fifth, we have resources, and resources is basically anything reusable. So, you can imagine it like a library of prompts, templates, frameworks, maybe content output examples, good examples, things like this. Then we have the skill folder, an important one,
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where the reference material of your skills live. For example, your strategy job docs, your voice guides, your ICP descriptions, basically additional information that your skills point to.
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So, you can see I have all my skills here with the reference files laid out.
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By the way, if you want access to all of the skills that me and my team are building out and using, you can also check out my AI accelerator in the link in the description. Then lastly, we have
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here tasks, and tasks can basically be a to-do lists, and then we have teams with more context around each team member's role and responsibilities in your business, so your agent always has context around anyone in your team. And
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that's really it. And then at the root here, you have the cloud.md file, the brain file, which is the instruction layer that tells your AI agent how this whole file system here works and how to navigate it. And this will also appear
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in the co-work section in the folder instruction that I showed you before. Now, if you're setting this up for yourself as a solopreneur or maybe as a professional, you can basically have the same structure but a little bit simpler.
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So, here I have an example of the personal OS. It's basically the same file structure without the department, without the team section, and without the onboarding. So, same file structure, just a bit simpler. Again, might look overwhelming, but I started this a few
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weeks ago with just files, and this sort of naturally grew, and a lot of this context has been created by my AI agent.
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And the plugin we built is going to make this process a lot easier and faster to do. So, how do we set it up? You can just go to Obsidian and download Obsidian for free. Once you've done that, you'll land on a screen like this.
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So, you can just go here to create new vault. For example, I call it Benny AI test.
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And then I have to choose a folder. So, I just create a new folder, and this is the folder that you're going to point Co-worker, Cloud Coder, any AI agent you use towards to access that same vault that Obsidian visualizes for you. So, we
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open this one and click create. So, we now have an empty folder. Now, if you're going to set this up in Cloud Coder, you can also use Obsidian CLI, which I'll make sure to put in the description below, that can help you get to a basic
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generic setup a bit quicker. But, as I said, we've built our own plugin, which is available in my AI Accelerator together with all our other plugins and skills to get you to that file structure that I showed you before a lot quicker.
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It helps you also populate your essential context a lot faster, and this plugin will work across Cloud Coder, Cloud Coder, wherever you want to use it. So, if that's interesting to you, you can check it out in my AI
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Accelerator in the link in the description below. We also have unlimited one-on-one live tech help available if you want some help setting up these things. We also do AI workshops where we dive a lot deeper into these setups and tools. So, if that's
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interesting, definitely check it out. Also, if you're a business and you want me and my team to help you in a more personalized way to set up a business AI OS for your company, we're now opening a few limited spots to help businesses set
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this up. So, if you want more information, you can also check the link in the description below. In there, you can find a link with the marketplace of plugins and skills of my accelerator.
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And from there, if you do it in Co-worker, you can just go to customize, click here on the plus, and you click add marketplace, and you add the link that you find in accelerator. Once you've done that and you go to browse
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plugins, you'll find a tab here at personal that says Binyan AI skills, and in there at the bottom, you'll find our plugin, Binyan Obsidian plugin. You can install that, and now you'll see that in your plugins, this one will appear.
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And there we have the skills that help you get to that setup in Obsidian a lot faster. And all we do then is we point Co-worker to the same folder that we just set up in Obsidian. So, in this
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case, Binyan test. We click always allow, and now we use the plugin and the skill setup.
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Right, we run this and it will walk you through the set up on getting to this file structure a lot faster and I'll start asking you some question to get the essential context set up. So, first it asked me what kind of file do I want?
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A business set up or a solopreneur set up? So, in this case I'll do solopreneur just to show you as an example.
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So, now it's already created the initial folder structure and the Claude MD with the instructions on how to navigate this type of folder structure. As you can see now in Obsidian, we already have this folder structure. Now, most of these are
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still empty of course because we haven't given Claude any context. So, the next question is to really start giving it context, right? And that's what this plugin does, right? It's going to ask you some questions to populate your
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initial context data set. Now, want to spend probably half an hour to an hour here to get your your initial set up, have the initial context data set and from there it will naturally expand and I can tell you if you start using AI
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more and more, in a couple of weeks you'll have a very expanded data set of context that really makes your AI far more powerful. So, couple of important things to keep in mind once you get to that initial data set is every new task
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you start in Claude Code, Claude Co-work, you always want to point towards that same folder. Second, when there are things that you want your AI or your second brain to remember, clearly tell Claude Co-work to remember this in your second brain or whatever
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you call your folder. If you can, ideally even point it to the specific file it has to save that rule to.
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Thirdly, if you see it have issues navigating the folder structure, tell it to update the Claude MD, which you can also do yourself because it remember this is the bridge to point it to the right direction. So, I can add in rules
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all the way at the end here, too. You can see I've already added some rules on how it should navigate the folder structure. And then lastly, if you're going to build skills, I highly recommend to take a new approach now and
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instead of embedding reference files into the scale here in Claude Co-worker in Claude Code, save the reference files in your second brain and let the scale point towards the right folders. You can also adapt your old skills by just
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telling Claude. For example, here I said, "Can you adapt my LinkedIn skill and create a new skill?" And gave it here a specific instruction. Instead of having the reference files in the skill, point towards the files in the Ben AI OS
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to get the additional info instead of having them saved in the skill. And again, the earlier you start with this, the more powerful your AI agent is going to get over the long term. So, highly recommend to start soon with
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this. Now, that's it for this video. Again, if you want access to all of the plugins, skills that me and my team are building out, plus unlimited one-on-one live tech help and AI workshops where we dive a lot deeper into these tools, you
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can check out my AI accelerator in the first link in the description. And if you're a business that wants a little bit more personalized help in setting this up for your business, you can check the second link in the description
Speaker A
below. Thank you so much for watching. If you want to learn more about Claude co-work, skills, plugins, etc., you can also check out the video here above.
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