# How Jinion works (/how-jinion-works)



Each message you send goes to the model together with what Jinion knows about you and your project. The model then
works in steps: it reads files, runs commands and edits code through Jinion's tools, until the task is done or it
needs you.

## What the model sees [#what-the-model-sees]

| Part                 | Where it comes from                                                                                                                                     |
| -------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------- |
| System prompt        | Written by Jinion: how to work, what to ask you before, which tools to use, git, how to talk to you                                                     |
| Environment          | The folder it works in, its git branch or the repositories in it, your platform, and the date. In a [worktree](/worktrees), that folder is the worktree |
| Project instructions | `AGENTS.md` and `CLAUDE.md` in the folder you started Jinion in. See [Write project instructions](/project-instructions)                                |
| Memory               | An index of the notes the agent keeps, one line each. See [Use memory](/memory)                                                                         |
| Skills and MCP tools | Listed by name, loaded only when used. See [Use skills and MCP servers](/skills-and-mcp)                                                                |
| The conversation     | Your messages, the agent's replies, and what the tools returned                                                                                         |

Nothing else goes in: Jinion keeps its own settings, and doesn't load other tools' settings files, hooks or global
instructions such as `~/.claude/CLAUDE.md`. To bring over the memory, skills and MCP servers you set up elsewhere, see
[Bring your Claude Code setup over](/how-to/bring-your-claude-code-setup).

## Tools [#tools]

The agent works through tools, and each call shows as a line in the conversation:

| Tool                     | What it does                                                           |
| ------------------------ | ---------------------------------------------------------------------- |
| Read, Glob, Grep         | Read files and search the project                                      |
| Edit, Write              | Change files; each change shows as a diff                              |
| Bash                     | Run commands, in the foreground or [the background](/background-tasks) |
| Web fetch and search     | Read pages and search the web; each shows what came back               |
| Agent                    | Hand part of the work to a subagent, shown as a live tree              |
| Ask                      | Ask you a question with options                                        |
| Todo                     | Keep a task list you can follow                                        |
| Remember, Recall, Forget | Save, read and drop [memory](/memory) notes                            |

## Who decides what runs [#who-decides-what-runs]

Reads always run. What else runs without asking depends on the [permission mode](/permission-modes) you pick. On top
of every mode, Jinion itself asks before a commit, unless you [turn that off](/permission-modes#stop-asking-before-commits),
and before anything changes outside your project. Full access is the one mode that asks nothing at all.

## Where your data lives [#where-your-data-lives]

Conversations, memory, settings, worktrees and logs live in `~/.jinion` on your machine. See [The \~/.jinion folder](/reference/jinion-folder).