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Stop the agent first, then investigate. Cancel its run or terminate its process, restrict network or account access if data may still be moving, preserve logs and timestamps, inspect repository and host changes, and only then restore files. If a token, key, password, or other credential might have been readable, revoke it and issue a narrowly scoped replacement.

An unexpected edit does not prove that an attacker was involved. Ordinary model mistakes, ambiguous instructions, prompt injection in content the agent reads, a compromised tool, and excessive permissions can produce similar symptoms. Treat the event as a potential security incident until you know what the agent could access and what it actually did.

First response: contain the agent before investigating

1. Stop execution using an enforceable control

Use the agent’s visible Stop, Cancel, or terminate control. If commands continue, stop the operating-system process using the process controls appropriate to your system. Do not rely on sending another message to the same agent as your only containment measure: a manipulated or malfunctioning agent can ignore that request, and a command already running will not necessarily be undone by a new prompt.

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Note the time you stopped it and whether a command was still active. If a build, script, upload, or deletion was in progress, the stopping point helps you reconstruct what may have completed.

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2. Restrict access when exposure is plausible

If the process could still read files or send data, disconnect or restrict the relevant network connection. Revoke access that appears exposed, but choose the least disruptive action that matches the evidence. Stopping every service or rotating every credential immediately can destroy useful evidence and interrupt unrelated work; leaving an active session connected can enlarge the damage.

3. Preserve a record before cleaning up

Write down the agent and model name, operating system, project path, start and stop times, visible commands, confirmation dialogs, alerts, and affected paths. Save available run logs and terminal output. Avoid deleting logs, clearing shell history, or resetting the project before you have reviewed them. This record is useful even when the cause turns out to be an ordinary mistake.

Establish what the agent could reach

Containment is easier to choose when you map the agent’s capabilities rather than guessing from the changed file alone. Record the following boundaries:

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  • Processes: Was the agent still running, and did it launch child processes, background jobs, installers, or scripts?
  • Filesystem: Which project directories, home-directory files, mounted drives, temporary folders, and ignored files were readable or writable?
  • Network: Could it make outbound requests, receive remote content, or reach internal services?
  • Identity: Which operating-system user, SSH keys, cloud profiles, package registries, source-control tokens, or service accounts were available?
  • External actions: Could it push code, open a ticket, send mail, publish an artifact, or modify a deployment?

Least-agency guidance from OWASP treats these boundaries as security controls: provide only the autonomy, tools, and access required for the task. A local agent that can edit one checkout is a different incident from one that can read a home directory and use production credentials.

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Possible causes are not interchangeable

The same symptom—an unexpected file or command—can result from:

  • a model misunderstanding an instruction or choosing an unsafe implementation;
  • an ambiguous request that allowed a destructive interpretation;
  • indirect prompt injection in an email, document, issue, web page, or repository file the agent consumed;
  • a compromised extension, tool, dependency, or integration; or
  • permissions broad enough that a small error had a large blast radius.

Do not label the event a compromise solely because the result was surprising. Conversely, do not dismiss it as a harmless hallucination until you have checked network activity, credentials, and external accounts.

Inspect changes without destroying evidence

In a Git repository

Run inspection commands from the affected checkout and save their output. Start with status, then examine both unstaged and staged differences:

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git status
git diff
git diff --cached

git status reports tracked changes in the index and working tree and identifies untracked files. git diff shows content differences that are not staged; git diff --cached shows what is staged for the next commit. Review filenames, permissions, renames, generated files, and unexpectedly large changes—not just source-code lines.

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Repository status is not a complete machine audit. Check ignored files and directories, files outside the checkout, editor or build caches, temporary archives, and deleted paths. A change in an ignored environment file can matter more than a visible source edit. Inspect the agent’s run log and shell history for commands that touched locations Git does not track.

When there is no repository

Compare affected files with a known-good backup, filesystem snapshot, or separately stored copy. Record modification times and ownership before opening files in an editor that might rewrite them. If the agent ran scripts, inspect those scripts and any output directories they created. Do not assume that an unchanged project folder means no data left the machine; uploads and copied secrets may exist elsewhere.

Build an event timeline

Put the agent start time, each visible command, file modification times, network alerts, process launches, and your containment actions in order. A timeline distinguishes a command the agent actually executed from text it merely proposed, and it highlights activity that continued after the first unexpected edit.

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Recover files selectively

Decide what to keep

Separate wanted work from unwanted work before restoring anything. Copy or commit the wanted changes to a safe branch or backup if doing so will not include secrets. Keep a copy of suspicious files for examination, but do not execute them. If the event may involve malware or a regulated dataset, involve your security or incident-response team before modifying evidence.

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Use Git restore with an explicit scope

Git documents that git restore replaces specified paths from a chosen source. For example, restoring one file from the current HEAD is explicit:

git restore --source=HEAD -- path/to/file

Restoring a path can remove it when that path is absent from the source. A broad restore or reset can overwrite legitimate work, staged content, or both, so preview the paths and source first. Restore only after you have preserved any changes you may need for analysis.

Recovering untracked or deleted data

Git cannot restore an untracked file that was never committed, and repository commands do not recover every deleted or external file. Use backups or filesystem recovery appropriate to your operating system. Treat commands that clean untracked files as destructive; do not run them merely to make git status look clean.

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Respond to possible credential exposure

When to revoke

Revoke a token, API key, password, SSH key, cookie, or cloud credential when the agent could read it and you cannot establish that it remained private. A secret in an environment variable, configuration file, shell history, ignored file, or mounted credential store should be considered reachable if the agent had permission to read that location.

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Revocation should match the credential’s scope. Disable the specific key or session first when possible, then review the account, service, and source-control activity associated with it. GitHub’s incident guidance, for example, distinguishes actions by disruption and threat evidence; other providers have different controls and audit views.

Replace with a narrower credential

Issue a new credential limited to the required repository, environment, operation, and lifetime. Prefer short-lived, task-scoped credentials over a personal or production-wide secret. Update the legitimate workflow only after confirming that the old credential is disabled, and remove exposed values from files, logs, and build artifacts. Rotating a secret without reducing its permissions leaves the same blast radius for the next incident.

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Recognize indirect prompt injection and excessive agency

NIST describes agent hijacking as indirect prompt injection: an attacker places instructions in material an agent may ingest, such as an email, file, or website. Its evaluation gave an agent command-line access to a Linux environment inside a container and tested an instruction that downloaded and ran a program from an untrusted URL. That setup demonstrates an attack pattern; it does not establish that an attacker caused your particular local change or indicate how common such events are.

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OWASP’s excessive-agency guidance focuses on damaging actions produced by unexpected, ambiguous, or manipulated model outputs. Its DevSecOps guidance states: “Permission prompts are not a security boundary against a manipulated agent; isolation is.” An approval dialog can be useful for review, but it is not a substitute for limiting filesystem, network, process, and identity access.

Choose containment according to evidence

What you observe Immediate action Likely disruption
The agent is still executing commands or spawning processes Terminate the process and its children; restrict network access if transfers are possible Stops the current task and may interrupt legitimate work
Files changed, but no network or credential access is indicated Preserve logs, inspect the worktree, and review local paths before restoring Usually limited to the affected project
A secret was readable and may have been used Revoke the specific credential, inspect provider activity, and issue a scoped replacement Dependent services may need reauthentication
External changes or data transmission are confirmed Contain the account or integration, preserve provider logs, and escalate to security personnel Can affect collaborators, deployments, or customers

Use the narrowest action that reliably stops ongoing harm. Increase disruption only when evidence shows a broader boundary was crossed.

Rebuild a safer local-agent setup

Control Practical configuration Trade-off
Isolation Run tasks in a disposable virtual machine, development container, or equivalent sandbox; destroy and recreate it for untrusted work Improves containment but can complicate hardware access, caches, and debugging
Filesystem scope Mount only the project and required scratch directories; keep home, backup, and production paths unavailable Some tools need additional paths, which should be added deliberately
Network egress Block outbound traffic by default and allowlist the package registries, APIs, or hosts the task needs Offline or restricted operation can break dependency downloads and integrations
Tool and command allowlists Permit only the interpreters, package managers, and actions required; deny installers, privilege escalation, and destructive commands unless separately reviewed Reduces automation convenience
Credentials Use short-lived, task-scoped secrets with the minimum repository and service permissions Requires a way to mint, deliver, and rotate credentials
Auditability Retain command, file, process, and network logs outside the agent’s writable area Consumes storage and may require privacy controls

Apply these controls before restarting. Configure the boundary outside the agent where possible, so the agent cannot simply approve its own expanded access.

Checklist before you let the agent run again

  1. Confirm the previous process and its child processes are stopped.
  2. Record the incident timeline and preserve relevant logs.
  3. Review Git status, diffs, ignored paths, external directories, and backups.
  4. Decide which changes are wanted and preserve them separately.
  5. Revoke any credential that may have been readable or used, then issue a scoped replacement.
  6. Inspect source-control, cloud, package, and service-account activity for unexpected actions.
  7. Move the task into an isolated environment with restricted filesystem and network access.
  8. Use an allowlist of tools and commands and keep audit logs outside the writable workspace.
  9. Start with a harmless, low-privilege task and verify the boundary before granting additional access.

When to escalate

Contact your organization’s security or incident-response team when a production credential, regulated or personal data, external account, deployment system, or customer-facing service may be involved. Escalate as well when you cannot determine what ran, when logs are missing, or when suspicious network or account activity continues after containment. Provide the timeline, commands, changed paths, credential scope, and containment steps; do not speculate about a cause that the evidence does not establish.

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