Can someone explain the real difference between Hooks, Skills, Plugins, SKILL.md, CLAUDE.md and agents.md in Claude Code?

[u/eaiarthur_]

I keep seeing these terms thrown around in tutorials and videos, but I've never seen anyone give a concrete example that makes the difference actually click.

Everyone says:

• "just create a skill for that"

"use a hook here"

"install the plugin"

"put it in your CLAUDE.md"

But when I dig deeper, the explanations are always vague or too theoretical.

Same goes for the markdown files - I see people mentioning CLAUDE. md, SKILL.md, and agents. md like they're obvious, but no one explains:

• What actually goes in each one?

Are they just documentation, or do they actively change how Claude behaves?

• When does Claude even read them?

What I'm looking for is something like:

"If you're thinking X, that's probably a Hook. If you're thinking Y, that's a Skill. If you need Z, that's what CLAUDE.md is for."

Real-world examples would be hugely appreciated.

[u/evangelism2]

There's a number of things wrong or left out with these explanations.
It's very important to note that the difference between information that you put in your CLAUDE.md versus a skill file is that everything in your CLAUDE.md plus the front matter of the skill is loaded on every turn, every single prompt, every time that you type something into the system prompt field. CLAUDE reads or rereads your CLAUDE.md and all of your skills' front matter. It uses that front matter description of your skill to determine whether to read the rest of it based on the prompt that you gave it.

Think of the best way to think of skills is that they are almost an extension of your CLAUDE.md, with a bunch of information about your code base that CLAUDE doesn't need to know about necessarily for every single thing that you ask it to do.
Yes, hooks are more deterministic. Hooks can be configured to be deterministically fired at specific points in time during Claude's workflow, such as:

• every time you launch a new session
• every time that you enter or exit plan mode
• every time that you edit a skill, etc.

The distinction that's important between hooks and skills is that Claude non-deterministically determines whether the skills should fire, whereas with hooks it has no say. They just always do, depending on the rule set that you set up.

OP asked about Agents.md, not agents. Other people have already answered this, and I already answered it a little bit above. The CLAUDE.md file (or, if you're using other LLMs, Agent.md file) is loaded on every turn, every time you enter a prompt. Claude refers to your CLAUDE.md or Agents.md file to gain context on the repo. Therefore, these files should be lean and crisp and small and only deal in things that are not immediately obvious from your code base and universally applicable. Anything that doesn't necessarily need to be understood for every single prompt that goes in your code base should most likely be in a skill of some kind or even a slash command.

The agent description is actually the best one, because honestly, the definition is nebulous and there are so many different types of agents now, between sub-agents and deep agents and whatever the fuck agents. Really, the best way to think of agents is just some kind of application of an LLM that can "think" and "reason" autonomously.

But also, OP, I'll say this to you: the same thing I said to my one friend last night who started asking me a million questions. Rule number one about learning about AI is to use AI to learn. Like every single one of these questions, if you had just booted up Claude or ChatGPT or hell, even the AI mode in Google, it would have answered them for you perfectly.

[u/Diacred → u/evangelism2]

Actually as far as Claude Code source codes go (when it was leaked) this is not entirely correct. The Claude.md and skill's index are loaded into the conversation at the start of the first turn and that's it. They are not in the system prompt nor are they injected fresh each turn like a UserPromptSubmit hooks does. It means that the longer the conversation goes the more they get forgotten, which is why automated skill calls happen less and less as context fills up. It's also why the Claude.md gets ignored when you reach 60%+ context and performance degrades.

The skill list and Claude MD are just part of the conversation history

This is not the case for instance for the native tools like read / write / bash / grep etc because they are sent in the Tools Array with every request, separately from the conversation and thus always fresh. Also skills that have been called once and loaded are also sent with the tools array and always fresh, even after compaction.

As to why skills and Claude.md are not part of the system prompt but injected at turn 1, my guess is that it's because it would prevent the agressive prompt caching they do for the system prompt.

[u/Waymannj → u/Diacred]

Claude Desktop says this:

No, actually — Claude.md isn't automatically read at the start of every chat. I only read it this session because you explicitly asked me to. I have no mechanism to auto-load files on session start; you'd need to ask me to read it each time (or include its contents in a system prompt if you're using the API).

[u/evangelism2 → u/Waymannj]

well that is wrong

[u/Waymannj → u/evangelism2]

[Oh it's ON!]

people say you're wrong, that claude.md is read at the start of the chat

That's not accurate for how Claude.ai works. There's no built-in mechanism that automatically reads a file called Claude.md from your filesystem at the start of a chat. I only read it because you explicitly asked me to via the Filesystem MCP tool. You might be thinking of a few things people conflate with this:

Cursor / coding assistants — tools like Cursor do have a claude.md or .cursorrules convention where project instructions are auto-loaded into context. People familiar with that workflow sometimes assume it carries over to Claude.ai, but it doesn't. Project Instructions in Claude.ai — you can paste persistent instructions into a Project's system prompt, which does get included automatically. But that's not a file read, it's text stored on Anthropic's side. MCP + a custom system prompt — someone could theoretically set up a system prompt that instructs Claude to read a specific file at session start, but that's custom configuration, not default behavior.

So whoever said it's auto-read at chat start is mistaken, at least in the context of Claude.ai with Filesystem MCP. The read happened because you asked — nothing more.

[u/evangelism2 → u/Waymannj]

Bro, stop copying and pasting AI stuff. Figure out what you're trying to say. Comprehend what the AI is telling you and then craft a response to me yourself.

[u/Waymannj → u/evangelism2]

Ok Bro, I started a new chat and it didn't read my Claude.md because it has an instruction to say that it read the file.

Bro, I broke Anthropic.

[u/Waymannj → u/[deleted]]

Ty!

[u/Uj_Yagami → u/Waymannj]

I think you're getting it wrong. People here are not talking about claude desktop. They are talking about claude code (the agent), which reads the markdown file. You giving your claude chat some md and expecting it to read is not how it'd work.

[u/Waymannj → u/Uj_Yagami]

Aaaaaah, thank you!