Put shared review guidance in a repository-root CLAUDE.md (or .claude/CLAUDE.md), keep personal preferences under ~/.claude/, and use .claude/rules/ for focused project rules. File access is controlled separately in settings with gitignore-style Read(...) and Edit(...) permission patterns. A review rule tells Claude what to inspect; a permission rule determines whether it may read or change a path.
Where each Claude Code rule belongs
Claude Code combines instruction files and permission settings, but they solve different problems. Choose the location by scope first, then by purpose.
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| Location | Scope | Best use | Shared through version control? |
|---|---|---|---|
CLAUDE.md at the repository root |
Everyone working in that repository | Build commands, coding standards, review criteria, required tests and project patterns | Yes |
.claude/CLAUDE.md |
Everyone working in that repository | An alternative project instruction location when you prefer a dedicated Claude directory | Yes |
~/.claude/CLAUDE.md |
One user, across projects | Personal style, preferred tools and recurring review habits | No |
.claude/rules/ |
One repository | Modular project rules such as security, API or migration checks | Yes |
~/.claude/rules/ |
One user, across projects | Private, reusable personal rules | No |
Project settings such as .claude/settings.json |
Tool access in that project | Allowing or denying reads and edits by path | Usually, when committed deliberately |
Anthropic’s GitHub Actions guidance specifically recommends a repository-root CLAUDE.md for coding standards, review criteria, project-specific rules and preferred patterns. Keep those durable expectations in source control; put the instruction for an individual pull request in the workflow prompt.
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Review rules are not ignore files
A review rule is prose that changes Claude’s evaluation. For example, “flag a database migration that has no rollback guidance” tells Claude what finding to report. An ignore-style permission rule is a boundary around tool access. Read(secrets/**) can prevent a read, while Edit(docs/**) can permit edits in documentation. One does not replace the other.
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- Use
CLAUDE.mdand files in.claude/rules/to define what good code looks like and what a review must check. - Use settings permission rules to control whether Claude can read or edit particular paths.
- Do not describe a sensitive directory as “ignored” in a review document and assume it is protected. Add an explicit deny rule.
- Do not put review criteria in a deny rule; a deny rule can block access but cannot explain the quality standard you want applied elsewhere.
Set up a durable project layout
A small repository can use one root file. A larger codebase benefits from focused rule files that can be changed independently.
repo/n├── CLAUDE.mdn├── .claude/n│ ├── CLAUDE.mdn│ ├── rules/n│ │ ├── review.mdn│ │ └── security.mdn│ └── settings.jsonn└── ~/.claude/n ├── CLAUDE.mdn └── rules/Use either the root CLAUDE.md or .claude/CLAUDE.md as the main project entry point; keeping two files with overlapping instructions makes conflicts harder to diagnose. Put narrowly scoped requirements in .claude/rules/. Name files for the concern they cover, such as security.md or review.md, rather than creating one large, contradictory rulebook.
Write a useful root CLAUDE.md
Keep the file concise and operational. State the commands a reviewer should run, the severity categories to use, the areas requiring extra scrutiny, the evidence expected from tests and the patterns that should trigger a finding.
Include commands and expected evidence
List the exact build, lint and test commands used by the repository, including any command that must be run for a changed subsystem. Explain what counts as sufficient evidence: for example, a focused test for changed API behavior plus the broader test suite when shared code is modified.
Define review findings precisely
Describe a finding in terms Claude can apply consistently: the condition to detect, why it matters, the severity and the expected remediation. “Check security” is too vague. “Report a high-severity finding when user-controlled input reaches a shell command without validated arguments; include the call site and a safer alternative” is actionable.
Mark sensitive areas
Identify directories that need extra scrutiny, such as authentication, payment, authorization, migrations or infrastructure. Explain project-specific invariants, generated-file conventions and patterns that should not be changed manually.
Avoid conflicting instructions
User rules load before project rules. If a personal preference conflicts with a repository requirement, Claude can behave inconsistently. Keep personal guidance generic and let the project file define non-negotiable conventions. Remove duplicate wording rather than adding a third rule intended to “win” an argument.
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Split rules when different teams maintain different concerns or when a rule applies only to a subsystem. A security file can require threat modeling for authentication changes; a review file can define severity labels and test evidence. Keep each file self-contained enough that a reviewer can understand the requirement without hunting through unrelated documents.
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Project rule files are still instructions, not access controls. If a rule says “never open production secrets,” enforce that requirement with a deny permission as well. Conversely, a permission deny does not tell Claude how to review the files it can access.
Control reads and edits with permission patterns
Read/Edit permission entries use the form Tool(optional-specifier) and follow gitignore-style path matching relative to the settings file. The documented examples include Edit(docs/**), Read(~/.zshrc) and Edit(//tmp/scratch.txt).
| Pattern | Meaning | Typical use |
|---|---|---|
Read(secrets/**) |
Matches files below a project-relative secrets directory |
Deny reads of checked-out secrets or secret fixtures |
Edit(migrations/production/**) |
Matches edits below the project’s production-migration directory | Require a human-controlled deployment process |
Edit(docs/**) |
Matches edits below the project’s documentation directory | Allow routine documentation changes |
Read(~/.zshrc) |
Uses a path relative to the current user’s home directory | Refer to one personal configuration file |
Edit(//tmp/scratch.txt) |
The leading // denotes an absolute path |
Permit or deny one exact location outside the project |
A leading ~/ means a home-relative path. A path without either marker is interpreted relative to the directory containing the settings file, so moving a settings file can change what a pattern matches. Review the resulting scope whenever you relocate settings.
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{n "permissions": {n "deny": [n "Read(.env)",n "Read(secrets/**)",n "Edit(migrations/production/**)"n ],n "allow": [n "Read(src/**)",n "Edit(docs/**)"n ]n }n}The exact settings structure and supported keys can vary with the Claude Code version installed. Check the documentation for that version before adding new keys, and test a rule against both a path that should match and one that should not.
Understand precedence before broadening access
Deny rules override allow rules. If a path appears in both lists, the deny wins. This makes broad allow patterns security-sensitive: an allow such as Read(**) can grant access to files you intended to protect unless a more specific deny reliably covers every sensitive location.
Settings also have an authority order. Enterprise-managed settings outrank CLI settings, local project settings, shared project settings and user settings. A local change cannot override a managed restriction. When a rule appears to be ignored, identify which layer supplied it before changing patterns.
| Higher priority | Lower priority |
|---|---|
| Enterprise managed settings | CLI settings |
| CLI settings | Local project settings |
| Local project settings | Shared project settings |
| Shared project settings | User settings |
Because permission rules govern access to source, credentials and generated artifacts, treat every broad allow as a security decision. Prefer the narrowest directory and tool scope that supports the task.
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Load reusable instruction fragments safely
Use an @path/to/import line in an instruction file when the same guidance belongs in several places. Imports can also point into a home directory for personal instructions. Recursive imports are limited to five hops, so a chain that exceeds that depth will not provide an unlimited hierarchy.
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Keep import graphs shallow and document why an imported file is shared. A practical arrangement is one root file importing one or two stable fragments, with those fragments containing no further imports. This makes the effective instruction set easier to audit and reduces surprises when a file is moved.
Handle monorepos and ancestor files
Claude Code discovers instruction files from the working directory and its parent directories. In a monorepo, an ancestor CLAUDE.md can therefore affect a package you thought was isolated. Use scoped files in each relevant .claude/rules/ directory, and inspect the loaded context from the package directory where you will run Claude.
Where supported, claudeMdExcludes can prevent unrelated ancestor instructions from being loaded. Organization-wide mandatory guidance in managed policy locations cannot be excluded by personal settings, so coordinate changes with the administrator rather than trying to bypass them locally.
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By default, Claude reads AGENTS.md when no CLAUDE.md, .claude/CLAUDE.md or CLAUDE.local.md exists on the working-directory path. Supported versions expose /config choices for combined or CLAUDE-only behavior. Because this behavior is version-gated, check the configuration available in the installed release and confirm the result with /context or /memory.
Configure a pull-request review in GitHub Actions
Keep stable review criteria in the version-controlled root CLAUDE.md. Use the workflow prompt for the immediate task: for example, review the pull-request diff, inspect the authentication subsystem, or report only regressions introduced by the change. This separation prevents temporary task wording from becoming permanent project policy.
- Commit the repository’s coding standards, review criteria, preferred patterns and required test commands in
CLAUDE.md. - Configure the workflow to start in the repository directory so Claude discovers the intended project instructions.
- Pass a focused prompt describing the pull request or subsystem under review.
- Ensure the workflow’s permissions permit the reads needed for review while denying secrets and protected edit paths.
- Review the workflow output for findings, severity, file locations and test evidence rather than treating a clean response as proof that every issue was found.
Separate interactive and automated configuration
An interactive session and a CI job can load different files and receive different permissions. Before diagnosing a discrepancy, compare the starting directory, the instruction files visible from that directory, and the settings layers active in each environment. A workflow prompt should identify the immediate pull request or subsystem; it should not replace the repository’s durable standards.
For non-interactive automation, review CLI controls such as -p, --allowedTools and --disallowedTools. These flags narrow or expand what the process can do for that invocation, but they do not rewrite the project’s review prose. Avoid bypass modes unless the execution environment is intentionally controlled, isolated and trusted. A repeatable CI job should make its working directory and tool permissions explicit rather than relying on a developer’s personal settings.
Use a path test matrix before committing settings
Permission mistakes often come from testing only the happy path. For each new rule, check an exact file, a nested file, a sibling directory and an absolute or home-relative path when relevant. For example, a deny on Read(secrets/**) should be tested against a file directly below secrets and one several directories deeper, while a nearby non-secret source file should remain readable if that is the intent.
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Test tools separately. Read(secrets/**) does not automatically deny Edit(secrets/**), and an edit allow does not grant read access. Likewise, a pattern relative to the settings file will not match a path outside that base unless you use the documented home-relative or absolute syntax. Record the intended result for each test so a future settings move or version upgrade can be checked against the same expectations.
Verify what Claude actually loaded
When Claude reads or edits a file that you meant to exclude, verify the effective configuration instead of guessing at pattern syntax.
- Start Claude Code from the intended repository or package directory.
- Run
/contextor/memoryand confirm that the expectedCLAUDE.mdand rule files appear. - Check parent directories for an ancestor
CLAUDE.mdthat adds instructions or changesAGENTS.mdhandling. - Search both user and project files for contradictory requirements, especially broad personal allows or instructions that tell Claude to inspect excluded paths.
- Inspect deny entries and precedence before broadening an allow pattern.
- Test the permission with a harmless path that should be allowed and a representative path that should be denied.
Troubleshoot common failures
Claude follows the wrong review standard
Look for duplicate or conflicting user and project rules. User files load before project files, but conflicting instructions can still produce inconsistent behavior. Move the repository requirement into the shared project file, remove the personal exception or rewrite both rules so they express one unambiguous policy.
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A denied file is still accessible
Confirm that the deny pattern is relative to the settings file, that the path uses the correct ~/ or // prefix when needed and that the entry names the correct tool. A deny for Read(secrets/**) does not automatically deny an edit, and a project-relative pattern does not match an unrelated absolute path. Check higher-precedence managed settings as well.
An allow rule unexpectedly opens too much
Replace broad globs with the smallest directory or file set that supports the task. Add explicit denies for secrets, production migrations and other high-impact locations, then test representative nested paths. Remember that a deny wins when both rules match.
A rule file seems invisible
Run /context or /memory from the directory where Claude starts. Check spelling, parent-directory discovery and whether an ancestor file or supported claudeMdExcludes setting changes what is loaded. If the file is imported, verify every import path and keep the chain within the five-hop recursive limit.
CI behaves differently from an interactive session
Compare the working directory, loaded instruction files and permission sources. A workflow prompt should supply task-specific direction, while the committed CLAUDE.md supplies durable criteria. For non-interactive use, review CLI flags such as -p, --allowedTools and --disallowedTools; avoid bypass modes unless the execution environment is intentionally controlled.
A maintainable configuration checklist
- Place shared build, test, coding and review guidance in a version-controlled root
CLAUDE.mdor.claude/CLAUDE.md. - Keep personal cross-project preferences in
~/.claude/CLAUDE.mdand~/.claude/rules/, not in the repository’s policy files. - Use
.claude/rules/to separate security, API, migration and other focused project concerns. - Use
Read(...)andEdit(...)permission entries for path access; do not confuse them with review criteria. - Check relative, home-relative and absolute path syntax before committing settings.
- Make deny rules explicit for secrets and protected production paths, and treat broad allows as sensitive.
- Resolve user/project conflicts and account for enterprise-managed precedence.
- Keep import chains shallow and within the five-hop limit.
- Use
/contextor/memoryafter changes, especially in monorepos. - Keep CI’s stable policy in source control and pass only task-specific direction in the workflow prompt.
Frequently Asked Questions
Where should shared Claude Code review rules go?
Put repository-wide coding standards, review criteria, preferred patterns and required test commands in a version-controlled root CLAUDE.md or .claude/CLAUDE.md. Use .claude/rules/ for narrower project concerns.
How do I make Claude Code ignore a file?
Use a permission deny entry for the relevant tool, such as Read(.env) or Read(secrets/**). A prose instruction saying not to open a file is not an access boundary, and a read deny does not automatically deny edits.
What is the difference between CLAUDE.md and .claude/rules?
Use the main CLAUDE.md for concise, repository-wide operating guidance. Use .claude/rules/ for modular files covering security, APIs, migrations or other focused topics that can be maintained independently.
Why is Claude reading a file I meant to exclude?
Check that the pattern is relative to the settings file, uses ~/ or // when appropriate, names the correct tool and is not being changed by a higher-precedence setting. Confirm loaded instructions with /context or /memory.
Do deny rules override allow rules?
Yes. A matching deny takes precedence over a matching allow. Because of that, broad patterns such as Read(**) should be treated as security-sensitive and tested against protected paths.
Can personal rules override a company-managed restriction?
No. Enterprise-managed settings outrank CLI, local project, shared project and user settings. Managed instructions also cannot be excluded through personal settings.
How many imported instruction files can be chained?
Recursive @path/to/import loading is limited to five hops. Keep import graphs shallow so the effective instructions remain easy to inspect and audit.
Why does a monorepo package inherit unexpected instructions?
Claude discovers instruction files in the working directory and its parent directories. An ancestor CLAUDE.md may therefore apply to a package. Start Claude in the intended package directory, inspect /context or /memory, and use supported claudeMdExcludes settings when unrelated ancestors must be omitted.
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Keep durable review guidance in a shared CLAUDE.md, split focused requirements into .claude/rules/, and enforce file boundaries with explicit Read(...) and Edit(...) permissions. Check path scope, precedence, imports and loaded context before trusting a rule, especially in monorepos and CI.
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