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Before a coding agent changes a file, make it explain what it thinks you want and how it intends to proceed. Ask for the expected files, behavior changes, assumptions, risks, and a read-only plan; correct the scope; then create a Git checkpoint and review the resulting diff and tests. This short pause improves communication and limits surprises, but it is not a guarantee that the agent understood the task or produced safe code.
Why an agent should explain itself before editing
File-editing agents can inspect a repository, choose an implementation, run commands, and modify several files in one turn. The dangerous mistake is often not a bad line of code; it is solving a different problem from the one the developer intended. A request to update one parser may lead to changes in tests, configuration, generated files, or an unrelated module if the agent infers a broader goal.
A pre-edit explanation creates a human checkpoint while the proposed change is still cheap to redirect. You can see whether the agent identified the right entry point, understood the desired behavior, and noticed constraints such as backward compatibility or a database migration. Treat the explanation as a communication aid, not as evidence that the plan is correct.
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Permission prompts are a separate usability issue. Anthropic’s Claude Code FAQ captures a common complaint: “It keeps asking permission for the same commands”. Reducing repeated prompts can make a session less frustrating, but it does not answer the more important question of what the agent should be allowed to edit.
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The checkpoint to request
Use a prompt that explicitly forbids edits until the plan is accepted:
Restate the goal in your own words. Which files do you expect to change, what behavior should change, what assumptions are you making, and what could go wrong? Do not edit yet; give me a read-only plan.This wording is a practical template, not a tested safety guarantee. Ask the agent to distinguish files it must change from files it may inspect. For a bug fix, require the expected failing behavior and the test that should demonstrate the fix. For a refactor, require an explanation of what must remain unchanged. For a configuration change, ask which environments and secrets are affected.
What a useful response contains
- Goal: a concise restatement of the requested outcome, including the user-visible behavior.
- Scope: paths the agent expects to read and paths it expects to modify.
- Mechanism: the proposed implementation and why it fits the existing architecture.
- Assumptions: versions, APIs, data formats, test fixtures, or conventions the plan relies on.
- Risks: compatibility breaks, destructive migrations, security implications, race conditions, or missing coverage.
- Validation: tests, linters, type checks, or manual checks that should run after the change.
How to approve or correct the plan
- Compare the restatement with the request. If the agent describes a different outcome, correct it before discussing implementation.
- Check every proposed path. An unrelated directory, generated artifact, lockfile, or deployment file deserves an explanation. A plan that omits the obvious implementation file may indicate that the agent has not located the feature correctly.
- Test the assumptions. Ask the agent to inspect a version declaration, interface, fixture, or call site in read-only mode when a plan depends on one. Do not approve an assumption merely because it sounds plausible.
- Look for omitted behavior. Ask how errors, empty input, permissions, retries, migrations, and rollback will behave when they are relevant to the task.
- Narrow the authorization. State which files and commands are in scope and prohibit unrelated cleanup, formatting, dependency upgrades, or generated-output changes unless they are required.
- Approve only after the plan is bounded. If the plan is still vague, request a more specific read-only investigation rather than granting implementation access.
Approval is not containment
Visual Studio Code makes the distinction explicit: “Approvals determine whether an action runs automatically or requires your confirmation.” Its documentation separately explains that sandboxing restricts the file-system and network resources terminal commands can access even after an action is approved. Read the full approvals and permissions documentation for the controls available in your installation.
In practice, an approval answers may this action run now? A sandbox answers what can that action reach? A plan checkpoint answers does this proposed work match the request? A diff answers what actually changed? You need all four questions for a reviewable workflow; one control cannot substitute for the others.
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How current tools expose planning, permissions and review
Mode names are not standardized. Compare the behavior documented for your installed version, workspace, organization policy, and plan rather than relying on labels such as “plan mode” or “agent mode.”
| Tool documentation | Read-only planning stage | Approval and permission behavior | Containment or review notes |
|---|---|---|---|
| Codex CLI | A read-only planning stage is not stated in the cited guide. | Documentation describes configurable permissions and commands. | The guide recommends Git checkpoints before and after a task and describes inspecting commands and diffs. |
| Claude Code | Plan mode is described as read-only and approval-gated. | Approvals last for the current session by default; the FAQ documents ways to persist allow rules. | Persistent rules should be limited to actions you intentionally allow. |
| Visual Studio Code agents | The cited approvals page does not establish a universal read-only plan mode. | Approvals determine whether an action runs automatically or requires confirmation. | Sandboxing separately restricts file-system and network resources available to terminal commands. |
| GitHub Copilot agents | The cited responsible-use guidance does not establish a common read-only planning stage. | Use the controls exposed by your repository and agent configuration. | GitHub warns that review can miss problems, especially in large or complex changes, so human review remains necessary. |
These differences are why a team policy should describe observable controls—read-only inspection, allowed paths, command confirmation, sandbox limits, and diff review—instead of requiring a particular product label.
Create a Git checkpoint before implementation
A clean starting point makes the agent’s work reversible and makes review easier. Codex’s CLI guidance recommends creating checkpoints before and after a task. In a repository where you are allowed to commit, first inspect the working tree and either commit existing work or record it separately so that the agent’s changes are distinguishable.
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git commit -m 'checkpoint before agent change'Do not commit unrelated or sensitive files merely to obtain a clean tree. If your team does not permit local checkpoint commits, create a branch, stash only appropriate work, or use the repository’s normal snapshot mechanism. The essential property is that you can identify and revert the agent’s changes without losing prior work.
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Approve a bounded implementation
After accepting the plan, restate the boundaries in the approval message: name the permitted files, the commands that may run, and the checks required before completion. Tell the agent to stop if it discovers a necessary change outside that scope. This turns a vague authorization into a conditional one.
Keep high-impact operations gated: deleting files, rewriting history, changing production infrastructure, rotating secrets, applying irreversible migrations, or sending network requests to systems outside the test environment. A sandbox can reduce exposure, but it does not make a destructive command appropriate.
Review the result, not just the explanation
- Inspect the diff. Look for changes outside the approved paths, accidental formatting churn, generated files, dependency updates, hard-coded credentials, and weakened validation.
- Compare behavior with the stated goal. Trace the changed code from input to output and check error paths, authorization, logging, and compatibility.
- Run focused checks first. Execute the relevant unit or integration tests, then the project’s normal type, lint, and build checks. A passing test suite does not prove that an unstated requirement was met.
- Review tests as code. Confirm that new tests fail for the old behavior and cover boundary cases; do not accept tests that merely reproduce the implementation.
- Inspect the final repository state. Use the post-change checkpoint or commit to preserve a known-good reference and make rollback straightforward.
GitHub’s responsible-use guidance cautions that AI review can miss issues, particularly in large or complex changes. Human review should therefore examine the code and its context, not simply accept an agent’s summary or an automated approval.
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When permission prompts repeat
Repeated prompts usually indicate a session or permission-setting choice, not a need to skip the pre-edit checkpoint. The Claude Code FAQ says approvals last for the current session by default and documents ways to persist allow rules. Persistent rules can reduce interruptions for routine, low-risk actions, but scope them narrowly: a read-only search command is different from a command that writes files, accesses the network, or changes deployment state.
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Before persisting a rule, ask three questions: Is the command predictable? Is its working directory constrained? Could a malicious file, shell expansion, or unexpected repository state turn it into a harmful operation? If any answer is unclear, keep confirmation enabled or use a sandbox.
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The plan names too many files
Ask the agent to justify each path and separate required edits from optional cleanup. Revert to read-only inspection until the list matches the feature boundary. If generated files must change, identify the generator and the command that will produce them.
The plan is confident but unsupported
Request evidence from the repository: the relevant interface, call sites, version declaration, or failing test. A plan based on an invented API or assumed directory structure should not receive write approval.
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The agent starts editing before approval
Stop the run, preserve the current diff, and inspect what changed. Restore from the pre-edit checkpoint if necessary, then restart with the tool’s read-only or approval-gated mode enabled. Do not continue merely because the first changes look harmless.
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The implementation passes tests but changes behavior elsewhere
Compare the diff with the original scope, run tests for neighboring components, and check public interfaces and configuration defaults. Ask for a focused follow-up plan rather than allowing broad cleanup in the same change.
A command requires access outside the sandbox
Identify exactly what resource is needed and why. Prefer a fixture, local mirror, or narrowly scoped permission. Approval should be granted only after you understand the data being read or modified and the consequences of the command.
What the available evidence does—and does not—show
Published studies support caution, not a causal claim that asking an agent to explain itself prevents defects. A 2026 exploratory study screened 36,710 repositories and found 85 repository-preserved agent plan files across 10 repositories. The authors, affiliated with the University of Bamberg, Heidelberg University, Singapore Management University, and King’s College London, describe that corpus as highly concentrated; see the study.
A separate 2025 study examined 567 Claude Code-assisted pull requests across 157 open-source projects. It reports that 83.8% were eventually accepted and merged, and that 45.1% of merged pull requests were integrated without further modification. Those percentages describe that sample and should not be treated as rates for every agent, repository, or task; see the study.
Neither study establishes that a particular prompt guarantees safe behavior. The practical case for a checkpoint is stronger as a process argument: it exposes misunderstandings before implementation, preserves human control over scope, and creates a natural place to enforce permissions and rollback.
A team policy you can adopt
- Every non-trivial file-editing task starts with a restatement, expected file list, assumptions, risks, and read-only plan.
- The requester confirms scope before write access is granted.
- Approval settings and sandbox limits are checked for the current session and workspace.
- A Git checkpoint exists before implementation, unless the project’s documented workflow provides an equivalent snapshot.
- The agent stops when it needs an out-of-scope file, command, network resource, or destructive operation.
- Reviewers inspect the complete diff and relevant tests; an agent summary is never the only review.
- Persistent allow rules are limited to predictable, low-risk commands and revisited when the tool, repository, or policy changes.
Tool defaults, plan access, permission behavior, and organization controls can change by version, subscription, rollout, and workspace policy. Check the documentation for the exact installation you are using, then keep the intent checkpoint, containment, and diff review as separate controls.
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