Claude Code

Claude Code is Anthropic’s coding agent and Marginal’s default. Its context lives in CLAUDE.md files and a .claude folder, in the project and in your home directory. A project without a CLAUDE.md gets its AGENTS.md read instead.

Select it in Settings ▸ AI ▸ Coding agent.

What Marginal lists

Section	In the workspace	In your home folder
CLAUDE.md	`CLAUDE.md` in the root and in any subfolder; `CLAUDE.local.md` beside it, badged local; `.claude/CLAUDE.md`. Where there is no `CLAUDE.md`: `AGENTS.md` and `.claude/AGENTS.md` instead, see below	`~/.claude/CLAUDE.md`
RULES	`.claude/rules/*/.md`	`~/.claude/rules/*/.md`
SKILLS	`.claude/skills/*/SKILL.md`	`~/.claude/skills/*/SKILL.md`
AGENTS	`.claude/agents/*.md`	`~/.claude/agents/*.md`
COMMANDS	`.claude/commands/*/.md`	`~/.claude/commands/*/.md`

CLAUDE_CONFIG_DIR, when set in the environment Marginal was launched from, replaces ~/.claude as the home-folder location.

Skills and sub-agents are named by the name: in their front matter, and show its description: as their second line. Rules keep their file name; commands appear as /name, with a subfolder in front as /folder/name.

AGENTS.md where there is no CLAUDE.md

Claude Code 2.1.277 and later read AGENTS.md, the file Codex, Cursor, and other agents use, in a project that has no CLAUDE.md. Marginal lists the files it would read, with Read in place of CLAUDE.md as their second line:

AGENTS.md and .claude/AGENTS.md at the root, when neither the root nor any folder above it has a CLAUDE.md, .claude/CLAUDE.md, or CLAUDE.local.md. Your ~/.claude/CLAUDE.md does not count, and is listed alongside.
AGENTS.md in a subfolder that has none of those three files of its own. A subfolder with its own CLAUDE.md shows that one instead.

One of those files at the root, or in a folder above the workspace, turns the fallback off everywhere, as it does in Claude Code. That includes a CLAUDE.local.md added for your own notes. AGENTS.local.md, AGENTS.override.md, and .agents/ are never read.

Claude Code’s Project instructions setting (/config) changes the rule. Marginal follows it when it is set in ~/.claude/settings.json:

Project instructions	What Marginal lists
`claude-md-or-agents-md`, the default	As above
`claude-md-and-agents-md`	Every `AGENTS.md` beside the `CLAUDE.md` files, with Read along with CLAUDE.md
`claude-md`, `managed-only`	No `AGENTS.md`

managed-only also leaves the project’s CLAUDE.md files out, which Marginal still lists. A value set in managed settings or with --settings is not visible to Marginal, and neither is the built-in agents-md plugin being turned off in /plugin. Marginal reads the setting whenever it scans the workspace, so after changing it, open the folder again.

How Claude Code uses these files

CLAUDE.md is loaded at the start of a session in this order: the managed file, ~/.claude/CLAUDE.md, then the project’s files from the outermost parent down, each followed by its CLAUDE.local.md. A CLAUDE.md in a subfolder is loaded on demand, when Claude reads a file there. @path lines import other files, up to four hops deep.
AGENTS.md, when it is read, loads the same way: the root’s and every parent’s at the start, a subfolder’s when Claude reads a file there. @path imports work in it too. A CLAUDE.md that imports @AGENTS.md still works, and never loads the file twice.
Rules in .claude/rules are markdown with an optional paths: list of globs in the front matter. A rule without paths: is loaded at the start; one with paths: is loaded when a matching file is read. Subfolders and symlinks are followed.
Skills are folders holding a SKILL.md plus any supporting files. The front matter gives the name, description, and whether the skill can be invoked by you (/name), by Claude, or both. Custom commands in .claude/commands are the older form of the same thing: still read, one /name per file, but new work belongs in skills.
Sub-agents in .claude/agents are markdown with a front matter name, description, and options such as tools, model, and memory; the body is the sub-agent’s system prompt.

The project-level files take precedence over the ones in your home folder when a name clashes.

Not listed

.claude/settings.json, settings.local.json, and ~/.claude/settings.json (including the hooks defined there), .mcp.json, output styles, workflows, worktrees, plugins, the auto-memory folder under ~/.claude/projects, and the managed paths under /Library/Application Support/ClaudeCode, /etc/claude-code, or C:\Program Files\ClaudeCode.

Checked against the Claude Code documentation on 24 September 2026.