The Tool Desk
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CLAUDE.md can tell Claude Code how your system is meant to fit together, but it cannot guarantee that a change respects those boundaries. Treat it as concise project guidance, then use hooks and permissions to control tool actions, architecture tests to catch forbidden dependencies, and sandboxing to limit what commands can reach.
What CLAUDE.md does—and does not do
Anthropic describes CLAUDE.md as project memory: context that helps Claude Code understand a repository and the team’s conventions. It is useful for build, test, lint, and run commands; coding standards; a short map of major components and their communication; hard constraints; and known gotchas. Keep it concise, accurate, and maintained like onboarding documentation. Anthropic suggests roughly 200 lines or fewer as a practical guideline, not a technical limit. Anthropic’s memory guidance
The important distinction is that a model-facing instruction influences choices; it is not a mechanical barrier. A sentence saying “core must not import database code” does not itself reject that import, block an edit, or fail a build when the dependency appears. Use the file to explain intent and point to the checks that enforce it—not as the only place the rule exists.
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| Control | Best used for |
|---|---|
CLAUDE.md |
Repository orientation, durable facts, conventions, commands, and architectural intent. |
| Path-scoped rules | Guidance relevant only to particular directories or files, such as API or migration constraints. |
| Skills | Reusable procedures that should load when needed, such as release or review checklists. |
| Hooks and permissions | Deterministically checking, gating, denying, or restricting tool use. |
| Architecture tests | Checking selected code-structure constraints, such as dependency direction or cycles. |
| Sandboxing and least privilege | Limiting which files, commands, and network destinations the agent can access. |
Anthropic’s June 18, 2026 steering guidance says, “A real guardrail needs to be deterministic, and the enforcement methods are hooks and permissions.” It also explains that a PreToolUse hook can inspect a tool call and deny it. These controls govern tool actions; they are not automatically comprehensive architecture verifiers. Check Anthropic’s steering guidance and the current Claude Code hooks documentation for current behavior and syntax.
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For organization-wide deterministic policy, Anthropic identifies managed settings as the mechanism local user configuration cannot override. Path-specific guidance and skills solve different problems: they improve relevance and reuse but should not be mistaken for enforcement.
Turn architectural boundaries into executable tests
Start with a few costly or security-relevant rules that can be checked from the code and build model. Examples include:
- Core or domain logic cannot depend on delivery, database, or framework code.
- Feature modules communicate only through declared public interfaces.
- Cycles between components are forbidden.
- Infrastructure access stays behind designated ports or adapters.
- Actual dependencies conform to a deliberately maintained component diagram.
These are starting points, not universal architecture prescriptions. Choose boundaries that reflect how your own system is meant to change and be maintained.
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For Java, ArchUnit’s 1.5.1 user guide documents rules for package and class dependencies, layer access, cycles, and conformance to PlantUML diagrams. One example allows services to be accessed only by controllers and other services. Because the rule examines imported Java classes, a violation can fail an ordinary test run instead of relying on an agent to remember a prose instruction.
ArchUnit is a Java example, not a universal solution. For other languages and build systems, assess whether a candidate tool can inspect the relevant dependency structure, integrate with the existing test and CI workflow, report the offending boundary clearly, and let the team revise rules as the design evolves.
Run checks where changes are delivered
Put architecture tests in the normal test path—locally and in CI where appropriate—and make failures identify the violating dependency or component. ArchUnit’s architecture-testing overview recommends expressing selected constraints as code and running them with each change. Review exceptions deliberately; update the tests when the architecture changes rather than preserving rules that no longer describe the system.
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A practical Claude Code workflow
- Document intent: Keep root
CLAUDE.mdfocused on key modules, permitted dependency direction, useful commands, and where the enforceable rules live. Avoid loading a large architecture specification as always-on context. - Scope detailed guidance: Put directory- or file-specific constraints in path-scoped rules. Put repeatable multi-step procedures in skills so they can be used when relevant.
- Constrain risky actions: Configure permissions and hooks for tool actions that must be restricted, checked, or denied. Use managed settings when policy must apply organization-wide.
- Test the architecture: Encode mechanically checkable boundaries and run them through the regular test runner and CI. Decide how exceptions are reviewed and how rules change with the design.
- Limit blast radius: Use sandbox filesystem and network restrictions and least-privilege access. These reduce what a misdirected or compromised agent can reach; they do not verify dependency direction.
- Review code and guardrails: Inspect changes to both the implementation and the rules intended to constrain it.
Why sandboxing is not an architecture test
Sandboxing restricts what commands and subprocesses can access, such as filesystem paths and network destinations. Architecture tests inspect whether code conforms to selected structural rules. Neither replaces the other: a dependency test does not protect secrets or restrict network access, while a sandbox does not detect that one module imports another against the intended design.
Anthropic’s October 20, 2025 engineering article reported an 84% reduction in permission prompts in its internal usage after sandboxing. That is a company-reported prompt-friction result, not a measurement of architecture compliance or prompt-injection prevention. Anthropic’s sandboxing article
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Account for untrusted content and human approvals
Instructions may be challenged by malicious content an agent reads, including text in emails, web pages, images processed through OCR, or tool output. Anthropic’s guidance recommends keeping untrusted content distinguishable from system instructions, limiting access to sensitive data and actions, using sandboxed tools and narrow permissions, and testing workflows with deliberate injection attempts. Anthropic’s prompt-injection guidance
A separate Anthropic article from 2026 reports that Claude Code users approve 93% of permission prompts. This is a vendor-reported figure about approvals, not evidence that approvals are safe or that architecture constraints are enforced. Anthropic’s auto-mode article
What a passing architecture test actually establishes
A green result means the rules you wrote passed against the code the test examined. It does not certify every desired quality attribute, prove the component boundaries are well chosen, or guarantee that runtime behavior matches the intended design. Teams still choose the constraints, review exceptional changes, and maintain the checks as the system evolves. The reviewed sources do not establish an independent statistic for how much CLAUDE.md alone protects architecture or a controlled violation-rate comparison with and without architecture tests.
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