The most effective setup uses two controls together: add friction before an agent can write or run something, and constrain the context it can read. In VS Code, use manual approvals, keep chat.editing.autoAcceptDelay at 0, leave edit-removal and retry confirmations on, and make sensitive-file globs such as **/.env explicitly non-approvable. In Cursor, choose Auto-review for a balanced default or a narrow Allowlist for predictable automation, set Read Access to Workspace, and enforce repository instructions with focused .cursor/rules/*.mdc files, AGENTS.md, and permissions.json.
These controls reduce accidental scope, secret exposure, and destructive commands. They do not prove that generated code is correct: accuracy still depends on the prompt, repository tests, human diff review, and the quality of the context supplied to the model.
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What to change first
If you want a short, safe baseline, make these changes before allowing an AI agent to work on a real repository:
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- Require deliberate edit acceptance. In VS Code, set
chat.editing.autoAcceptDelayto0. In Cursor, avoid Run Everything and use Auto-review or an empty Allowlist. - Protect sensitive paths. Do not auto-approve edits to
.env, secret stores, production configuration, generated output, lockfiles, or migrations unless the task explicitly names them. - Limit what the agent can read. Set Cursor Read Access to Workspace and use
.cursorignoreand repository permissions to exclude secrets, build artifacts, and unrelated directories. - Put durable instructions in the repository. Keep focused rules in version control so every contributor and agent sees the same conventions.
- Review the complete diff and run existing checks. Approval is a safety gate, not a code-review substitute.
Setting names and defaults can change between VS Code and Cursor releases. Check the current Settings UI and documentation for the version installed on your machine before copying a configuration verbatim.
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Why approval and context settings improve results
Unwanted edits usually come from one of two failure modes. The first is execution overreach: an agent accepts its own patch, runs a broad command, or retries a failing operation without giving you a useful pause. The second is context contamination: the model reads unrelated generated files, stale notes, secrets, or hostile instructions embedded in a comment or tool output and then makes a larger or less relevant change.
Approval controls address the first problem. Context boundaries and rules address the second. Neither setting changes the underlying model, and there is no established percentage that converts a particular setting into an accuracy improvement. Treat the configuration as risk management: it narrows the ways an incorrect response can become an unwanted repository change.
VS Code: settings for deliberate edits
Disable automatic acceptance of suggested edits
Set chat.editing.autoAcceptDelay to 0. VS Code documents 0 as the default; it disables automatic acceptance of suggested edits so you can inspect the patch before it is applied. A nonzero delay creates a countdown, which is still automatic acceptance and therefore a poor choice for sensitive repositories.
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{
"chat.editing.autoAcceptDelay": 0
}Workspace settings are easier for a team to audit, while user settings are useful when you want the same caution level in every project. Do not put secrets in either file.
Keep confirmation for removing and retrying edit requests
Leave both of these settings enabled:
{
"chat.editing.confirmEditRequestRemoval": true,
"chat.editing.confirmEditRequestRetry": true
}Removal confirmation prevents an edit request from disappearing when you click the wrong control. Retry confirmation adds a second decision point before the agent regenerates a patch, which matters when a retry could broaden the change or repeat a destructive command.
Show a file-change summary after each request
Enable chat.checkpoints.showFileChanges when you want a visible summary at the end of a chat request:
{
"chat.checkpoints.showFileChanges": true
}Use the summary as a review index, then inspect the actual diff. A summary can miss semantic problems, generated-file churn, or a change made by a tool outside the chat panel.
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Use an explicit edit auto-approval map
chat.tools.edits.autoApprove accepts glob patterns that determine which file edits can be approved automatically. The safest general policy is an empty map, which leaves edits for manual approval. If your workflow needs limited automation, allow only low-risk paths and explicitly deny sensitive ones.
{
"chat.tools.edits.autoApprove": {
"**/.env": false,
"**/.env.*": false,
"**/secrets/**": false,
"**/production/**": false,
"**/generated/**": false
}
}Pattern behavior is release-sensitive, so test each glob against a disposable workspace. Add variants for files your repository actually uses, such as .env.local, platform-specific secret directories, or deployment manifests. A false entry should be treated as a protected boundary, not as permission to read the file.
Do not auto-approve broad patterns such as **/* merely to remove prompts. If a task legitimately requires a migration, lockfile, or generated file, approve that one request and review the resulting diff.
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VS Code: terminal and tool permissions
Keep terminal auto-approval narrow
chat.tools.terminal.autoApprove is an allowlist for commands or command patterns. Keep it limited to read-only, deterministic checks that your project uses regularly. The documented defaults avoid automatically approving high-risk commands including rm, rmdir, del, kill, curl, wget, eval, chmod, and chown. Preserve those protections.
For maximum friction, disable terminal auto-approval altogether:
{
"chat.tools.terminal.enableAutoApprove": false
}If you keep it enabled, allow only commands such as your test runner, formatter, or type checker, and scope them to the repository. Avoid allowing a shell interpreter, command substitution, network downloader, package installer, or commands that write outside the workspace.
Do not enable global auto-approval
Keep chat.tools.global.autoApprove set to false. VS Code warns that global auto-approval disables critical security protections. A global switch can silently widen permissions for tools you did not intend to trust, especially after an extension or workspace adds a new capability.
{
"chat.tools.global.autoApprove": false
}Choose Manual permissions instead of Allow all or Autopilot
Manual permissions are the default approval model and the right starting point when minimizing unwanted edits. Allow all and Autopilot skip confirmation for potentially destructive actions. Use them only in an isolated, disposable environment where you have accepted that the agent may write or execute without a prompt.
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When VS Code asks for approval, inspect the tool name and every parameter. Depending on the prompt, approval may apply to one use, the current session, the workspace, or future invocations. Choose the narrowest scope that completes the task.
VS Code: reduce context contamination
VS Code documentation identifies prompt injection and context contamination as risks that can arrive through files, comments, or tool output. Keep the agent inside the workspace when possible, use sandboxing, select only the tools required for the task, and store credentials in the editor’s secure secret mechanisms rather than in repository text.
A practical request sequence is:
- Open the specific folder that contains the project; do not open a parent directory containing unrelated repositories.
- Ask the agent to list the files it plans to inspect before requesting an edit.
- Confirm that the list excludes
.env, credential stores, build output, and unrelated applications. - Ask for a small patch and a diff summary.
- Run the repository’s existing formatter, type checker, and tests after reviewing the patch.
These steps make the model’s context observable. If a file contains instructions that conflict with your request, treat them as untrusted content and do not grant extra permissions because the file asks for them.
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Cursor: choose a run mode that matches your risk tolerance
Auto-review for most interactive work
Cursor describes Auto-review as “the safest useful setup for most people.” It allows known-safe calls, sandboxes shell commands where possible, and routes higher-risk calls to a classifier. Choose it when you want fewer prompts without surrendering every decision.
Allowlist for deterministic automation
Use Allowlist when only a small set of repeat actions should run automatically, such as a particular test command or formatter. An empty Allowlist means every call requires approval, which is appropriate for a new repository, unfamiliar code, or a task involving deployment configuration.
Keep the list specific. Allowing a package-manager executable may also permit scripts or network access triggered by that executable, so prefer a project-specific command and review its arguments.
Avoid Run Everything for this goal
Run Everything executes every tool call automatically, without sandbox or classifier review. It is incompatible with the objective of reducing unwanted edits and should be reserved for disposable environments where the repository and credentials have no value.
Cursor: set a workspace read boundary
Set Read Access to Workspace when the agent should not read outside the repository without approval or an explicit allowlist. Workspace mode limits searches and sandboxed command visibility, reducing accidental discovery of sibling projects, home-directory credentials, or unrelated configuration.
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Pair the boundary with .cursorignore and repository permissions. Exclude secret files, dependency caches, compiled output, logs, large fixtures, and generated documentation that does not help the task. Ignoring a path reduces context exposure; it is not a replacement for filesystem permissions or secret rotation.
Cursor states that configuration-file changes require approval, while ordinary workspace files may be written without approval. Auto-reload can execute a configuration change before you review it, so disable or tightly control auto-reload in sensitive projects.
Cursor rules that keep edits in scope
Use focused, version-controlled project rules
Project rules live in .cursor/rules as .mdc files. A rule can be Always Apply, Auto Attached by glob, Agent Requested by description, or Manual through @rule. Cursor documentation describes rules as system-level instructions for the Agent.
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Example always-on guardrail
---
description: Repository editing guardrails
globs:
alwaysApply: true
---
- Read the relevant files before editing.
- Do not modify generated files, lockfiles, migrations, or .env files unless the request explicitly names them.
- Make the smallest patch that satisfies the request.
- After editing, summarize changed files and run the repository's existing checks.Use additional glob-scoped rules for areas with different conventions, such as frontend components, database migrations, or infrastructure. A path-scoped rule should state both what the agent may change and what it must leave alone.
Use AGENTS.md for repository-wide conventions
An AGENTS.md file is useful for concise instructions that should apply across tools: supported runtimes, test commands, naming conventions, generated-file policy, and definition-of-done checks. Keep it factual and maintainable. Put detailed, path-specific behavior in .cursor/rules rather than turning one file into an encyclopedia.
Cursor permissions.json: block dangerous actions explicitly
User-level ~/.cursor/permissions.json and project-level .cursor/permissions.json are merged; team configuration takes priority. Add plain-English block_instructions for actions that must never run automatically:
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"autoRun": {
"allow_instructions": [],
"block_instructions": [
"Every command that deletes files must go through approval first.",
"Never modify .env, secrets, production configuration, or generated files without approval."
]
}
}Use allow_instructions only for narrow, well-understood operations. A block instruction should name the action and the protected paths; “be careful” is not an enforceable boundary. Because team configuration takes priority, verify the effective settings when a workspace behaves differently from your local policy.
VS Code and Cursor compared by control surface
| Control | VS Code | Cursor | Practical choice |
|---|---|---|---|
| Edit acceptance and diff review | chat.editing.autoAcceptDelay, edit-removal and retry confirmations, and checkpoint file-change summaries. |
Run mode plus review of workspace diffs; ordinary workspace writes may not prompt. | Require manual acceptance for sensitive work and inspect the complete diff. |
| Terminal and tool autonomy | Narrow chat.tools.terminal.autoApprove; disable with chat.tools.terminal.enableAutoApprove; keep global auto-approval off. |
Auto-review, Allowlist, or Run Everything, with classifier and sandbox behavior depending on mode. | Use Auto-review or an empty/narrow Allowlist. |
| Persistent project instructions | Workspace settings and repository guidance supplied in context. | .cursor/rules/*.mdc, AGENTS.md, User Rules, and Team Rules. |
Keep concise conventions in version control and scope them by path. |
| Read boundaries and sensitive files | Workspace-limited access, sandboxing, tools picker, and secret storage. | Read Access to Workspace, .cursorignore, repository permissions, and approval for configuration changes. |
Exclude secrets and generated content; grant the smallest readable area. |
A repeatable safe-edit workflow
- Define the boundary in the request. Name the files or directory that may change, the files that must not change, and the checks to run.
- Confirm access settings. In VS Code, verify manual permissions, zero auto-accept delay, protected edit globs, and terminal policy. In Cursor, verify Read Access to Workspace, Auto-review or Allowlist, and effective project permissions.
- Ask for a plan before a patch. Require the agent to identify relevant files, dependencies, and likely tests. Reject a plan that includes unexplained directories or secrets.
- Approve the smallest operation. Approve a read, test, or one edit separately when possible. Do not approve a whole session merely because the first command was safe.
- Inspect the diff immediately. Look for unrelated formatting, renamed files, lockfile changes, generated output, and edits outside the requested path.
- Run established checks. Use the repository’s existing test, lint, formatter, and type-check commands. Treat a passing check as evidence about that check, not proof that the design is correct.
- Commit only after review. Keep permission files and rules in the same review process so a future change cannot silently widen autonomy.
Common failure modes and fixes
The agent still changes files without a prompt
Check whether the edit was accepted by a previous session, whether a workspace setting overrides your user setting, and whether the tool is writing through an extension rather than the chat edit mechanism. Set chat.editing.autoAcceptDelay to 0, remove broad edit auto-approval patterns, restart the workspace, and test with a harmless file.
A protected file is still appearing in context
An edit deny rule does not necessarily prevent reads. Add the path to .cursorignore, tighten Read Access to Workspace, remove the file from the opened folder where practical, and revoke or rotate credentials if a secret was exposed. In VS Code, use the tools picker and workspace boundary rather than relying on an edit prompt alone.
A retry makes the patch larger
Keep chat.editing.confirmEditRequestRetry enabled. Before approving, rewrite the request with explicit files, exclusions, and acceptance criteria. Ask for a minimal diff instead of repeating the same broad prompt.
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Inspect the complete command and arguments, including scripts invoked by package managers. Remove shell interpreters, downloaders, recursive deletion, permission changes, and process-control commands from automatic approval. Run the command manually in an isolated environment if it is genuinely required.
Rules are ignored or applied in the wrong directory
Check the rule’s front matter, glob, and activation mode. Split a broad rule into smaller path-scoped files, ensure the file is inside .cursor/rules, and commit the rule so teammates use the same version. Ask the agent to state which rule it applied before editing.
A practical policy by repository type
| Repository | VS Code policy | Cursor policy |
|---|---|---|
| Learning or disposable example | Manual edit review; narrow test-command auto-approval is acceptable. | Auto-review with Workspace read access; no secret files. |
| Production application | Zero auto-accept delay, protected sensitive globs, terminal auto-approval disabled or tightly allowlisted, global auto-approval off. | Auto-review or empty Allowlist, Workspace read access, blocking permissions, and mandatory diff review. |
| Infrastructure, deployment, or security code | Manual approval for every edit and command; isolate credentials and deployment directories. | Empty Allowlist, explicit block instructions, no Run Everything, and human approval for configuration changes. |
Maintain the controls as the tools change
Review settings after editor upgrades, extension updates, repository moves, and changes to team policy. Defaults, labels, experimental flags, and Cursor run-mode behavior are release-sensitive. Test the effective policy in a disposable branch: request a harmless edit, a protected-file edit, a read outside the workspace, and a destructive-looking command. Each should produce the prompt or block you expect.
Finally, treat permission configuration as code. Review changes to settings.json, .cursor/rules, AGENTS.md, .cursorignore, and permissions.json in pull requests, and remove temporary exceptions when the task ends.
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