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Use the lightest arrangement that matches the consequence of a write. Plan mode is appropriate for a one-off read-and-reason task. Deny rules make a project- or user-level prohibition repeatable. A separate, read-only filesystem or disposable copy is the stronger boundary for irreplaceable datasets. Hooks can enforce a team policy, but they must be implemented and tested for the tools and indirect command paths your installation exposes.
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A safe, no-write workflow in six steps
- Start from a controlled directory. Open Claude Code in the project that contains the scripts you want analyzed, but do not place the only copy of irreplaceable data inside that project. Put the authoritative dataset in a separate location or use a disposable working copy before you begin.
- Launch the session in plan mode. The CLI supports selecting a permission mode, and Anthropic describes plan mode as allowing analysis without modifying files or executing commands. The CLI reference is the authority for the flag spelling in your installed release: Claude Code CLI reference. Do not select an edit-accepting mode for this workflow.
- Ask for analysis, not remediation. State that the task is read-only and request a report, diff proposal, or list of commands for a human to run later. A proposed patch is information; applying that patch is a write operation.
- Inspect the effective policy. Run
/permissionsinside Claude Code and review the active permission mode, allowed tools, denied tools, and rules inherited from the project or user scope. This catches a configuration that is broader than you intended. - Add an explicit deny for recurring work. If the same project will be analyzed repeatedly, configure deny rules for the file-editing and other write-capable tools exposed by your release. Anthropic documents that deny rules take precedence over allow rules. The IAM documentation explains the rule model and scopes: Claude Code identity and access management.
- Separate the filesystem for high-consequence work. Keep the source dataset outside the startup directory when practical, restrict it with the operating system, or analyze a disposable copy. This is an additional boundary, not a replacement for Claude Code permissions.
These steps deliberately separate temporary session behavior from durable policy and from filesystem protection. If one layer is misconfigured, the others can still reduce the chance that a mistaken request, an inherited rule, or a command with side effects changes the original material.
What the Claude Code controls actually do
Plan mode: the simplest analysis-only choice
Plan mode is designed for understanding a task before implementation. Anthropic’s IAM material describes it as a mode in which Claude can analyze but cannot modify files or execute commands. That makes it the natural choice when you need code reading, data-structure inspection, dependency reasoning, or a proposed approach without an edit. The CLI reference documents permission-mode selection and should be checked against the release installed on your machine because option names and behavior can change: CLI usage documentation.
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Plan mode is a session-level control. It is easy to apply to a single audit, but it does not by itself create a durable project policy or protect files from other programs running under your account. It also does not make a prompt-skipping configuration safe. In a no-write workflow, leave edit-accepting behavior disabled and do not use --dangerously-skip-permissions; the CLI reference warns that this option skips prompts and should be used with caution.
Deny rules: a repeatable prohibition
A deny rule tells Claude Code that a selected action is not permitted. For a research project, deny the edit and write tools that your installed release makes available, and consider commands that can create, truncate, rename, or delete files. Tool identifiers and settings syntax are release-sensitive, so use the current IAM and CLI documentation rather than copying an old settings file. The important property is precedence: Anthropic states that deny rules win when an allow rule would otherwise grant the same action.
Use deny rules at the narrowest scope that still fits the work. A project-level restriction is useful for a repository where analysis is common; a user-level restriction is appropriate when every project on an account must be read-only. A one-off command-line restriction can protect a single invocation. Whichever scope you choose, inspect the result with /permissions instead of assuming that a file was loaded or that a parent configuration was replaced.
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Prompts are a consent checkpoint, not a permanent prohibition. A user can approve a write accidentally, and a broad allow rule can make a later prompt disappear. The CLI reference lists --allowedTools, --disallowedTools, and --permission-mode; use these only with the tool names and syntax documented for your installed version. For a no-edit session, prefer an explicit denial or plan mode over relying on a person to reject every prompt.
Avoid broad Bash approvals in a read-only workflow. A shell command can write indirectly through a script, redirect output, invoke a formatter, update a cache, or call another program that changes files. If command execution is genuinely needed for analysis, run it outside the protected tree or in an isolated copy and inspect its effects afterward.
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The startup-directory boundary
Anthropic’s security documentation describes file writes as confined to the startup directory and its descendants unless explicit permission is granted. That boundary can reduce accidental access to unrelated locations, but it should not be described as an absolute security barrier. It does not protect a file that is already inside the writable tree, and it is not an operating-system access-control policy. Read the current security guidance for the exact release and deployment context: Claude Code security documentation.
Use the boundary as one layer: start Claude Code in a purpose-built analysis directory, keep the canonical dataset elsewhere, and mount or copy only what the analysis requires. If a script needs to be inspected, provide a read-only copy of the script. If reports must be generated, direct them to a separate output directory that can be deleted without affecting the source.
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Anthropic’s IAM material describes PreToolUse hooks as running before ordinary permission evaluation and being able to approve or deny a tool call. A team can use a hook to check paths, reject write-oriented operations, record decisions, or require an additional review condition. Hooks are valuable when a policy needs organization-specific logic that a simple allow or deny rule cannot express.
A hook is custom enforcement, not a guarantee supplied by the documentation. The cited material does not establish that a particular hook covers every indirect write path, subprocess, or future tool. Maintain the hook like security-sensitive code: define the paths and operations it covers, test approved and rejected cases on a disposable copy, log decisions, and review it after Claude Code upgrades. Keep a separate filesystem control for data whose loss would be unacceptable.
Choosing the right combination
The following comparison is a practical decision aid based on the documented behavior and the extra setup each layer requires; it is not a benchmark or a guarantee of resistance against every attack.
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| Control | Typical scope | What remains available | Resistance to accidental or indirect writes | Setup and maintenance |
|---|---|---|---|---|
| Plan mode | One session or invocation | Reading, reasoning, and plan or diff proposals; no file modification or command execution as described by Anthropic | High for that session when correctly selected; does not protect against other processes | Low; verify the mode after launch |
| Deny rules | Project, user, or invocation, depending on where configured | Analysis and any tools not covered by the deny list | High for the named tools; coverage depends on whether all write-capable paths are denied | Moderate; review inherited rules and update identifiers when releases change |
| Startup-directory boundary | The Claude Code working tree and descendants | Operations permitted inside that tree | Useful for limiting reach, but weak when sensitive files are in the tree or a command has side effects | Low; choose the startup directory carefully |
| Operating-system permissions or isolation | Files, directories, users, containers, or virtual machines | Only what the operating system grants to the process | Strong independent boundary; can also block legitimate reads or writes if configured incorrectly | Moderate to high; requires administration, testing, and recovery planning |
| PreToolUse hook | Tools and conditions implemented by your policy | Whatever the hook approves | Customizable; effectiveness depends on implementation and coverage | High; requires code ownership, tests, logs, and upgrade review |
Setting up a one-off read-only analysis
Prepare a copy and define the output
Before launching Claude Code, decide which files are inputs and where any human-authored notes will go. For sensitive research, make a copy with the same directory structure but without credentials, unpublished identifiers, or unrelated projects. Mark the copy as disposable and reserve a separate output directory for the final report. This makes it possible to discard an unexpected change without reconstructing the original dataset.
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Start in plan mode
Use the CLI’s documented permission-mode option to select plan mode. Because the exact invocation can vary by release, confirm the current command in the CLI reference rather than relying on a remembered example. Once the session opens, ask Claude Code to summarize files, trace data flow, identify likely bugs, or propose a patch without applying it.
Check the active permissions
Run /permissions and read the displayed configuration. Confirm that the session is in the intended mode and that no inherited setting has enabled an edit-oriented mode or a broad command allowance. If the display does not match your expectation, stop the analysis, correct the configuration, and start a fresh session.
Review the result as an artifact
Save the explanation or proposed diff outside the source tree. If you need to test a suggestion, do so in a new disposable copy, not by switching the protected session into an edit-accepting mode. Compare the copy with a known checksum, version-control status, or file inventory before and after the test. Those checks are operational safeguards you control; they are not claims that Claude Code has performed a particular test.
Building a persistent project or user policy
Inventory every way a write could occur
List the operations your team considers a modification: editing source files, creating new files, deleting or renaming paths, changing permissions, writing generated data, and running commands that perform any of those actions. Include scripts that mutate databases, notebooks that save outputs, formatters, package managers, and tools that update caches. The goal is to deny capabilities, not just a single visible editor action.
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Apply deny rules at the appropriate scope
Use the current IAM documentation to configure denies for the relevant tools at project scope or user scope. Do not paste a settings example from an older release without checking its syntax. A deny should remain effective even if an allow rule is inherited, because Anthropic documents deny precedence. If the project needs occasional maintenance, create a separate, explicitly writable workflow rather than weakening the analysis policy for everyone.
Inspect inherited configuration
Open Claude Code and run /permissions after changing the policy. Look for rules inherited from the user profile, project, or a parent directory. Verify both the intended denial and the tools that remain available. Keep a short record of the policy owner, scope, date, and Claude Code version so a future upgrade can be reviewed instead of silently changing the workflow.
Test on a disposable fixture
Create a small fixture containing a script, a data file, and a directory that should remain untouched. Ask for analysis that would normally tempt a write, such as fixing a syntax error or exporting a cleaned table. Confirm that the session produces a proposal rather than changing the fixture. Test indirect cases separately, such as a command that redirects output or a script that writes beside its input. Dispose of the fixture after the test and repeat it when the CLI or policy changes.
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Keep the canonical copy outside the project tree
The documented startup-directory boundary is most useful when the authoritative files are not descendants of that directory. Store the canonical dataset in a location governed by your operating system or storage service, and expose only a read-only export or disposable copy to Claude Code. Keep credentials and unrelated repositories out of the analysis directory as well.
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Choose read-only access deliberately
Operating-system permissions, read-only mounts, separate user accounts, containers, or virtual machines can prevent a process from changing protected paths even if an application-level policy is wrong. Configure the process with the minimum read access it needs. Test that Claude Code can read the intended files while a harmless write attempt is rejected by the operating system. Record how an authorized researcher can create a new analysis copy; a protection that nobody can recover from becomes an operational problem.
Separate source, temporary files, and outputs
Some analysis tools write temporary files, indexes, logs, or caches even when the source data is unchanged. Point those locations to a disposable workspace. Put generated reports in a separate output directory and treat them as new artifacts. If a script must be executed, run it against a copy with no secrets and verify where it writes before allowing it to run.
When a hook is worth the maintenance
Use a PreToolUse hook when the policy depends on conditions such as path classification, file extensions, ticket numbers, or a review decision that simple tool denies cannot express. For example, a team might reject any operation whose resolved path is under an evidence directory while permitting analysis artifacts under a scratch directory. The IAM documentation establishes the hook’s place before ordinary permission evaluation, but not universal coverage of every possible write path.
- Define the protected roots and the operations that are forbidden.
- Resolve relative paths and symlinks before making an allow or deny decision.
- Fail closed when the hook cannot determine the target safely.
- Log the tool, path, decision, and policy version without recording sensitive data unnecessarily.
- Test direct edits, shell redirection, generated files, renames, deletes, and subprocesses on a disposable fixture.
- Review the hook after every Claude Code upgrade and whenever new tools are enabled.
Do not treat a hook as a substitute for operating-system permissions. A defect in custom policy can otherwise become the single point of failure.
Common failure modes and fixes
| Symptom | Likely cause | Fix |
|---|---|---|
| Claude Code asks to edit a file during an analysis session | The session is not in plan mode, or the requested action is outside the intended policy | Stop, inspect /permissions, restart in plan mode, and add a persistent deny if the restriction must recur |
| A write is still possible through a command | The policy denied an editor tool but left a shell or other write-capable path available | Inventory indirect operations, deny the relevant tools, and run command-based tests on a disposable copy |
| An inherited setting appears to allow too much | Project and user scopes were not reviewed together | Use /permissions to inspect effective rules; rely on explicit denies and remove unnecessary broad allows |
| Analysis cannot read a protected file | The operating system or isolation layer removed read permission, or the file is outside the permitted scope | Grant only the required read access to a copy, or move the analysis into an approved read-only workspace; do not make the canonical file writable just to solve the error |
| Unexpected files appear beside the source | A tool created caches, logs, temporary files, or generated output | Redirect temporary and output paths to a disposable directory and inspect scripts for side effects before execution |
| A hook blocks legitimate work or misses an indirect write | The custom policy does not handle a path form, subprocess, or newly introduced tool | Capture the failing case in a fixture, update the policy and tests, and keep filesystem isolation for high-value data |
Practices that make the policy durable
- Pin the workflow, not an undocumented settings file. CLI flags, rule names, settings syntax, and hook details are volatile. Check the live documentation that matches the installed release before publishing internal instructions or automation.
- Keep analysis and implementation sessions separate. Use a read-only project or account for investigation, then have a human review a proposed patch in a separately authorized workspace.
- Minimize tool access. Allow only the tools needed for the question. Avoid
acceptEdits, broad Bash approvals, and prompt-skipping options when the purpose is to prevent writes. - Make the safe path the easy path. Provide a standard project template with a scratch directory, a documented plan-mode launch procedure, and a visible permission check.
- Recheck after upgrades. The available tools and permission labels can change. Repeat the fixture test and review the current CLI, IAM, and security pages after an upgrade.
- Plan recovery. Keep versioned or immutable copies of important research data, record checksums where appropriate, and document who can restore an authorized copy. Prevention reduces risk; it does not replace backup and recovery.
What not to rely on
A confirmation prompt is not a durable control because it depends on a person making the right decision every time. A working-directory boundary is not an absolute barrier because files inside that tree remain in scope and explicit permissions or other processes may change the situation. Plan mode is not a replacement for operating-system protection when the data is irreplaceable. Conversely, making an entire account read-only can prevent legitimate analysis outputs and create pressure to bypass the policy. Match each control to a defined threat and keep the protections independent where the consequence justifies it.
A maintenance checklist
- Record the Claude Code version and the documentation version used for the procedure.
- Confirm the intended permission mode at the start of every sensitive session.
- Run
/permissionsand review inherited project and user rules. - Confirm that all known edit, delete, rename, generation, and command-based write paths are denied or isolated.
- Verify that the canonical dataset is outside the writable project tree or protected by the operating system.
- Use a disposable fixture to test direct and indirect write attempts after policy changes.
- Review PreToolUse hooks, logs, and test coverage when tools or releases change.
- Store reports and temporary files separately from source data.
Anthropic’s published material documents the existence and intent of these controls, but the cited pages do not provide a universal configuration that fits every release or environment. Treat the live documentation for your installed version as authoritative, and treat your own fixture tests and operating-system policy as the evidence that the combined workflow behaves as intended.
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