AI Coding Agent Terms Explained in Plain English

If you work with an AI coding agent, you will hear words like repository, branch, pull request and context window. This guide explains the ones that matter in plain English, with everyday comparisons, so you can follow a status update and ask better questions. You do not need to use these words yourself, but knowing them makes it much harder for a vague answer to slip past you.

The explanations follow how GitHub (a popular service for storing and reviewing software projects) and Claude Code (Anthropic's AI coding agent) describe things in their own documentation. Git is the standard tool for tracking changes to software, and GitHub's pages on it are the source for the first group of terms.

Where the work lives

What is a repository?

A repository is the project's home. According to GitHub's documentation, it is the entire collection of files and folders for a project, along with each file's revision history. Think of a shared drive for one product, where every older version of every file is kept too.

People often shorten it to "repo". When someone says "the agent has access to the repo", they mean it can read and change the project's files.

What is a commit?

A commit is a saved snapshot of the project at one moment. GitHub describes commits as snapshots in time that record the project's file history. Each one usually comes with a one-line note saying what changed.

Why you care: commits are the receipts. If something breaks on Tuesday, the list of commits shows what changed on Monday and who or what changed it.

What is a branch?

A branch is a separate line of development. Commits can be arranged into several lines, and people use them to work on changes separately before combining them. Picture photocopying a contract to mark up your edits, rather than scribbling on the signed original.

The original line is usually called "main". An agent can do its work on a branch so that a half-finished idea does not touch the version people rely on. Claude Code can also run several sessions at once by giving each its own directory for its own branch, so the sessions do not get in each other's way.

What is a pull request?

A pull request is a proposal to merge changes into the project. GitHub describes it as the place where people discuss and review changes before they are merged. It is the "please check this before it goes in" step.

On a pull request, a reviewer can read the description and comments, see which lines changed, and look at the results of automated tests and builds. A pull request can also be opened as a draft, which is shared early and cannot be merged until it is marked ready for review.

What does "merge" mean?

Merging means folding the changes from a branch back into the main line. On a pull request, GitHub shows a merge status that lists blockers, missing approvals and other requirements. If your team has a rule such as "two approvals and passing tests", that is where it shows up.

How the agent works

What is an "agentic" tool?

A plain chatbot answers with text. An agent can act. Claude Code's documentation says it works through three phases: gather context, take action and verify results. These blend together, and you can interrupt at any point.

For a request like "fix the failing tests", the documentation describes the agent running the tests, reading the errors, finding the relevant files, editing them and running the tests again. It is closer to a junior colleague working through a checklist than to a search box.

What is a tool, in this context?

Tools are the things the agent can do: read and edit files, search, run commands, look things up on the web. The documentation puts it directly: without tools, Claude can only respond with text; with tools, it can act. This is why permissions matter. Every tool is something you may or may not want used unattended.

What is a context window?

The context window is the agent's working memory for the current conversation. Claude Code's documentation says it holds the conversation history, file contents, command outputs, instruction files, saved notes, loaded skills (reusable instructions for particular jobs) and system instructions.

It fills up as you work. When it nears the limit, Claude Code clears older tool output first and then summarizes the conversation if needed. Your requests and key code snippets are kept, but the documentation warns that detailed instructions from early in the conversation may be lost.

Everyday version: a whiteboard that is only so big. When it is full, someone wipes the old notes and keeps a summary. If a rule matters, do not leave it on the whiteboard.

What is a session?

A session is one conversation with the agent, tied to one project folder. The documentation states that each new session starts with a fresh context window, without the history of earlier ones. That is a common reason an agent can seem to "forget" yesterday's decision.

What is an instruction file (CLAUDE.md or AGENTS.md)?

It is a plain written document in the project that Claude Code reads at the start of every session. Teams use it for coding standards, architecture decisions and review checklists. If a project already has an AGENTS.md file written for other coding agents, Claude Code can read that instead. Think of it as the onboarding sheet a new hire gets on day one. If your rules live only in chat, they are not durable.

What is a subagent?

A subagent is a helper the main agent sends off to do part of a job. The documentation says it works in its own context window, its tool calls stay out of the main conversation, and the main agent gets back a summary when it finishes. It is like handing a colleague a sub-task so your own desk stays uncluttered.

What is MCP?

MCP, the Model Context Protocol, is described in the docs as an open standard for connecting AI tools to external data sources. With it, Claude Code can read design documents in Google Drive, update tickets in Jira or pull data from Slack. In plain terms: a plug that lets the agent reach your other tools. Each plug you add is also one more thing it can touch.

Safety and control

What is a permission mode?

A permission mode sets what the agent may do without asking. The Claude Code documentation lists these:

• Auto: a classifier reviews most actions in the background and blocks the risky ones instead of asking you.
• Manual: Claude asks before file edits and shell commands.
• Accept edits: Claude edits files and runs common file commands without asking, but still asks about other commands.
• Plan: Claude explores and proposes a plan without editing your source files.

The practical question for you: which mode is the team using, and who chose it?

What is a checkpoint, and can I undo anything?

Before Claude edits a file, it saves a snapshot of the contents. If something goes wrong, you can rewind. This only covers file changes. The documentation is explicit that actions affecting remote systems such as databases, APIs and deployments cannot be checkpointed. You control those with the permission mode and permission rules.

So "we can undo it" is true for a bad edit to a page, and not automatically true for data deleted from a live database. Ask which kind of change you are talking about.

Quality and release

What are tests and checks?

Tests are small automated programs that confirm the software still does what it should. "Checks" is the broader word for anything automated that runs on a change, such as tests or builds. On a pull request, GitHub shows their results in a Checks tab. A passing check is evidence, not proof: it only covers what someone wrote a test for.

What is "production"?

Production is the live version real customers use, as opposed to a copy used for trying things out. A release is the moment a change goes there. Because it affects real people and data, the go-ahead should come from a person.

How Atlas fits in

Atlas is a software team of AI engineers built on Claude Code. You talk to its project assistant, called PA, in plain words, so you can run a project without using most of these terms. Each engineer works in its own copy of the code, and tasks sit on a board where you can see them move. Finished work is merged by a step Atlas calls the landing train, which merges up to six finished branches and runs the project's own checks once on the result.

Atlas does not yet explain terms such as branch, merge or checks where they appear on screen. Short plain-English explanations in the app are coming to Atlas, built in, so they will need no setup. Until then, ask PA to explain any word in plain terms. The Atlas home page is at /atlas/.

A short conclusion

Most of this vocabulary is ordinary project management dressed up: a shared folder, a working copy, a snapshot, a request for sign-off. If you remember only three ideas, make them these: work happens on a branch, not on the live version; the agent's memory is limited, so write down what matters; and undo has limits, so ask what is reversible before approving anything that touches live data. When an update uses a word you do not know, ask for the plain version. A good team can give you one.