Template L · Concept · D3 Agent Operations

CLAUDE.md Hierarchy.

7 min read·10 sections·Tier A

CLAUDE.md is persistent project memory loaded automatically by Claude Code. A three-level hierarchy (user → project → directory) lets you set global defaults, team standards, and per-directory rules. Project-level files are version-controlled and shared. Use @import to keep CLAUDE.md modular.

Project memory standardDomain 3Three-level cascade
CLAUDE.md Hierarchy — hero illustration featuring Loop mascot in a warm gallery scene.
Domain D3Agent Operations · 20%
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01 · Summary

TLDR

CLAUDE.md is persistent project memory loaded automatically by Claude Code. A three-level hierarchy (user → project → directory) lets you set global defaults, team standards, and per-directory rules. Project-level files are version-controlled and shared. Use @import to keep CLAUDE.md modular.

3
Hierarchy levels
2
File locations
@import
Import syntax
D3
Exam domain
,
Hard rule limit
02 · Definition

What it is

CLAUDE.md is a configuration file for Claude Code that defines project rules, conventions, and architectural decisions. It's not a .gitignore or a README, it's a working set of instructions that Claude reads every time it edits code or runs a command. The hierarchy has three levels: user (~/.claude/CLAUDE.md, your personal defaults), project (.claude/CLAUDE.md or root CLAUDE.md, shared rules), and path-specific (.claude/rules/*.md with glob frontmatter, rules for specific files).

The content is free-form Markdown but structured: stack info, test commands, code-style rules, key architectural decisions, gotchas, and @import directives that pull in modular rule files. Claude parses it as plain text, there's no schema validation, so mistakes in naming or structure cause silent ignores. The real power is reusability: rules travel with the code (version-controlled in .claude/), every teammate sees them on git clone, and new team members onboard faster.

Path-specific rules use YAML frontmatter with a paths glob array. When Claude edits a file matching the glob (e.g. **/*.test.tsx), that rule file auto-loads alongside the project CLAUDE.md. This enables scoped rule enforcement without drowning the main CLAUDE.md in per-file details. A testing rule file specifies pytest/Jest conventions, coverage thresholds, naming, all loaded only when you touch a test file.

Production misuse centers on scope creep (main CLAUDE.md becomes 500 lines of every possible rule) and rule inheritance traps (team expects user rules to apply but they don't, user rules are personal, project rules are shared). A contributor clones the repo, uses their personal style from ~/.claude/CLAUDE.md, and produces inconsistent code. The fix is always: put team rules in `.claude/CLAUDE.md`, never in user files.

03 · Mechanics

How it works

When Claude Code starts, it loads CLAUDE.md in order: (1) reads user ~/.claude/CLAUDE.md (personal defaults); (2) reads project root .claude/CLAUDE.md or root CLAUDE.md (shared); (3) while editing a file, checks all .claude/rules/*.md files, tests the paths glob against the filename, and loads matches. All loaded content is concatenated and injected as context into Claude's system prompt. The result is a layered set of rules: personal, then project, then path-scoped.

When a .claude/rules/*.md file contains @import ./subdir/rules/testing.md, Claude resolves the import and inlines that file's content. This prevents the main CLAUDE.md from exploding; rules live in modular files and compose via import. Circular imports are not detected and will hang the load. A production gotcha if you @import a file that imports its parent. Keep the import graph acyclic.

Path-specific rules are scoped via glob frontmatter. A testing rule file declares paths: ["**/*.test.tsx", "**/*.spec.ts"]. When you create or edit a file matching either glob, the rule auto-loads. Token-efficient: irrelevant rules don't load, keeping context focused. A migration rule (paths: ["migrations/*.sql"]) only loads when you touch SQL files.

Claude reads CLAUDE.md once at startup, not continuously. Changes require a session restart (or a manual reload command in newer versions). This is a UX tradeoff: rules are stable within a session (no surprise mid-conversation changes), but editing CLAUDE.md does not take effect immediately. Plan edits before sessions, not during.

CLAUDE.md Hierarchy mechanics, painterly diagram featuring Loop mascot.
04 · In production

Where you'll see it

Open-source repo onboarding

New contributor clones the repo. Project CLAUDE.md auto-loads: stack, test commands, code-style rules, key decisions. Saves a 30-min onboarding email per contributor. Rules travel with the code; nobody works from outdated docs.

Monorepo with subteam directories

Frontend team has rules in app/.claude/CLAUDE.md (component patterns, testing conventions); backend has api/.claude/CLAUDE.md (db migration discipline, error handling). Root CLAUDE.md holds shared rules. Editing inside app/ loads frontend rules; inside api/ loads backend rules.

Personal vault across many projects

Solo dev keeps personal preferences in ~/.claude/CLAUDE.md (preferred indent, commit message format). Each project repo has its own root CLAUDE.md with stack details. Switching projects: project rules change automatically; personal style stays consistent.

05 · Implementation

Code examples

Project CLAUDE.md skeletonmarkdown
# Project: PrecisionCare Navigator

## Stack
- Python 3.11 + FastAPI + Postgres
- React 19 + ShadCN + Tailwind
- Claude Opus for medical NER
- AWS ECS + RDS, region us-east-1

## Commands
- Dev: `make dev` (FastAPI :8000, React :3000)
- Test: `pytest -v --cov=app`
- Lint: `ruff check . && black --check .`
- Deploy: `make deploy ENV=staging`

## Code style
- 4-space Python (Black), 2-space React (Prettier)
- Type hints on every function (mypy strict)
- Named exports only
- Server actions for mutations; route handlers for queries

## Key decisions
- All patient data encrypted at rest and in transit
- Never log PII (mask in middleware)
- Async background work via Celery + Redis (not asyncio in FastAPI)

## Modular rules
@import ./rules/testing.md
@import ./rules/healthcare-compliance.md
@import ./rules/api-design.md

## Don't
- Add new endpoints without a corresponding test
- Mock the database in integration tests
- Commit secrets (use .env.example as the template)
Project CLAUDE.md should fit in ~1000-1500 tokens. Use @import for modular rule files. Lives at repo root, committed to git, shared with the whole team.
Path-scoped rule file (loaded only when editing matching files)markdown
---
paths: ["tests/**/*.py", "**/test_*.py"]
---

# Test Rules, auto-loads only when editing test files

## Naming
- Files: test_<module>.py (mirrors source file path)
- Functions: test_<function>_<scenario>
- Fixtures live in conftest.py at the deepest applicable level

## Patterns
- Use pytest.parametrize for data-driven cases
- Each test asserts ONE behavior (fail message tells you what)
- Mock external services with respx (httpx) or responses (requests)

## Anti-patterns
- Tests that depend on execution order
- Tests that read `os.environ` without monkeypatch
- Snapshot tests checked in without explicit PR review
- `time.sleep` in tests (use freezegun)

## Coverage
- Floor 85% per module
- Branch coverage on policy-critical files (auth, refund, billing)
Path-scoped rules in .claude/rules/*.md auto-load only when matching files are open. Keeps the always-on context lean while enforcing per-folder discipline.
06 · Distractor patterns

Looks right, isn't

Each row pairs a plausible-looking pattern with the failure it actually creates. These are the shapes exam distractors are built from.

Looks right

Put all team rules in ~/.claude/CLAUDE.md so they live with each developer.

Actually wrong

User-level files are personal and not in the repo. Team rules belong in project-level CLAUDE.md (root, committed). Otherwise new team members miss them.

Looks right

Document every framework convention exhaustively in CLAUDE.md.

Actually wrong

CLAUDE.md is appended to every prompt. Bloated files burn tokens and dilute attention. Keep it concise (~1500 tokens). Use @import for modular detail; link to long-form docs.

Looks right

Embed API keys in CLAUDE.md so Claude has them on every session.

Actually wrong

CLAUDE.md is committed to git. Secrets leak. Use environment variables and reference them in CLAUDE.md by name (e.g., 'OPENROUTER_API_KEY required in env').

07 · Compare

Side-by-side

MechanismScopeShared?Loaded whenBest for
~/.claude/CLAUDE.mdAll your projectsNo (personal)Every sessionPersonal preferences, indent style
./CLAUDE.md (project)One repoYes (in git)Every session in repoStack, commands, team standards
.claude/rules/*.mdPath-glob scopedYes (in git)When editing matching filesPer-folder conventions (tests, api/)
Skills (.claude/skills/)Task-scopedYes (in git)When task description matchesReusable workflows (PR review, etc.)
08 · When to use

Decision tree

01

Does this rule apply to everyone on the team?

YesProject CLAUDE.md (root) or .claude/rules/. Both committed to git.
NoPersonal preference → ~/.claude/CLAUDE.md.
02

Does the rule apply only to certain file types or directories?

YesUse .claude/rules/<topic>.md with frontmatter paths: [...]. Loads on demand.
NoProject CLAUDE.md root.
03

Is it a reusable workflow (e.g., PR review process)?

YesMake a Skill in .claude/skills/, not a CLAUDE.md addition.
NoEmbed in CLAUDE.md.
09 · On the exam

Question patterns

CLAUDE.md Hierarchy exam trap — painterly cautionary scene featuring Loop mascot.
A teammate's PRs use a different code style than yours. They have rules in `~/.claude/CLAUDE.md` but not in the repo. Fix?
Move team rules to .claude/CLAUDE.md (project root, version-controlled). User-level rules are personal; only project rules are shared via git. Team standards belong in the repo.
You add a rule to `.claude/CLAUDE.md` mid-session. Claude doesn't follow it. Why?
CLAUDE.md is loaded once at session start. Mid-session edits don't take effect until restart. End the session, restart, and the new rules apply.
Your testing rule file sits in `.claude/rules/testing.md` but doesn't auto-load when editing test files. What's missing?
Check the YAML frontmatter paths glob. Make sure it matches your file paths exactly. Try paths: ["**/*.test.tsx", "**/*.spec.ts"] for broad coverage.
You have `@import ./shared.md` in two CLAUDE.md files, and `shared.md` has `@import ../main.md`. Claude Code hangs on load. Why?
Circular import. Claude Code does not detect cycles. Refactor: don't have child rule files import their parents. Keep the import graph acyclic.
A new contributor follows the README but writes code that violates project conventions. They don't read CLAUDE.md. Architectural fix?
CLAUDE.md auto-loads when they use Claude Code, no reading required. If they bypass Claude Code (write by hand), enforce conventions via linters and CI checks. CLAUDE.md complements but doesn't replace tooling.
Your project root `CLAUDE.md` is 1,500 lines and Claude's responses are getting slower. Why?
CLAUDE.md is appended to every prompt. 1,500 lines is too much. Modularize: move detailed rules to .claude/rules/*.md with paths globs. Keep root CLAUDE.md to ~300 lines of universal team rules.
A path-scoped rule file's `paths: ["src/**/*.ts"]` matches but the rules don't apply to a file in `src/lib/utils.ts`. What's wrong?
Glob syntax. ** matches multiple directory levels, so src/**/*.ts should match src/lib/utils.ts. If not, check for typos in the glob or restart Claude Code.
You want different rules for `api/` (backend) and `app/` (frontend). Best structure?
Two path-scoped rule files: .claude/rules/backend.md with paths: ["api/**"], .claude/rules/frontend.md with paths: ["app/**"]. Keep root CLAUDE.md for shared rules. Each rule auto-loads only when relevant.
10 · FAQ

Frequently asked

If I have project + directory CLAUDE.md, which wins?
Both load. Directory rules apply only inside that directory; project rules apply everywhere. They are scoped, not conflicting.
What goes in user-level CLAUDE.md?
Personal preferences that don't vary by project, your indent style, commit message format. Not team standards.
Does CLAUDE.md affect performance?
Slightly, it appends to every prompt. Keep it concise; use @import if it grows past ~1000 lines.