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When an AI coding agent cannot use a tool or finish an action, troubleshoot the failure in layers rather than reinstalling everything. First identify the exact symptom, then verify the account, workspace, plan, model and integration are available. Next check provider authorization, pending approval, sandbox policy, network access and the MCP server’s status. Finally determine whether the model failed to invoke a healthy tool, correct the reported issue, restart the affected server or session, and retry.
A visible integration does not prove that every operation is supported. Read permission may not include write permission, and an approved command can still be blocked by a sandbox or network rule. The steps below apply to coding agents running in editors, terminals, hosted workspaces and remote execution environments; labels and commands differ by harness.
What exactly is failing: a missing tool, a denied command, or a server problem?
Write down the agent or harness, the requested action, the tool name, the exact error text and the point at which execution stopped. Classify the symptom before changing configuration because each class has a different owner and remedy.
- Tool missing: The tool or integration is not listed, has disappeared from the session, or the agent reports that no such capability exists.
- Tool not invoked: The server is available, but the model responds without calling the tool. Reinstalling the integration will not fix a model-selection or prompt-routing problem.
- Connection or authentication failure: The server cannot start, sign in, reach a provider, or validate a certificate.
- Approval pending: The product is waiting for you or an administrator to approve a particular operation.
- Command denied: A sandbox, workspace policy, provider permission or safety control rejected the operation.
- Partial completion: The tool ran but lacked a required file, parameter, destination or provider-side capability.
Capture the error before retrying. A message such as “permission denied,” “network unreachable,” “tool unavailable” or “approval required” is more useful than a general statement that the agent is broken.
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Is the agent, account, plan and workspace actually eligible to perform the action?
Confirm that the feature is offered on the current product surface and that the session is using the intended identity. Availability can depend on the signed-in account, subscription plan, geographic region, workspace, administrator settings, selected model, provider requirements and whether the integration is enabled for that organization.
Verify the active identity
- Open the account or profile menu in the editor, agent client or hosted workspace.
- Check the signed-in email, organization and workspace name.
- Compare them with the account that owns the repository, cloud resource or connected provider.
- Sign out and back in only if the displayed identity is wrong or the provider token has expired; repeated reconnects do not create a permission that the account does not have.
Check product and workspace availability
Look for an administrator-controlled setting that enables apps, MCP servers, extensions, shell access or external connections. An integration can appear in a marketplace or configuration file while remaining disabled by an organization policy. A feature may also be available in one editor surface or model but not another.
Distinguish installation from availability
An installed extension, listed plugin or saved server entry proves only that configuration exists. It does not establish that the current plan, region, workspace or provider supports the requested operation. If the feature is unavailable at that layer, changing permissions or reinstalling files is the wrong remedy; ask the workspace or provider administrator whether the capability is enabled.
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Does the integration support this action, and is the authenticated account authorized?
Check the operation itself, not just the connection. A connected app may be able to read data while being unable to create, edit, send or delete it. Read access does not imply write access, and a token valid for one project or repository may not cover another.
Map the requested action to a supported operation
- Reading a file, issue or record is different from changing it.
- Creating a pull request, sending a message or deleting a resource may require separate scopes.
- Listing resources can succeed while opening, modifying or deploying one fails.
- A provider may restrict actions by repository, branch, project, environment or role.
Inspect the integration’s permission or capability page and compare it with the exact operation in the error. Do not infer support from a tool’s broad name such as “repository,” “cloud” or “database.”
Check provider-side authorization
Open the provider’s account, organization and project permissions. Confirm that the authenticated identity has access to the named destination and that required scopes were granted during sign-in. If an administrator must approve an app, the agent cannot bypass that requirement. Reauthorize only after confirming which scope or organization is missing, and avoid granting broad access when a narrower project or repository permission is sufficient.
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Is an approval waiting, or is a safety control blocking the action?
Approval and sandboxing are separate controls. Approval determines whether an operation may run automatically or requires confirmation; sandboxing limits what an already-approved command can read, write or reach.
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- Open the approval request and read the complete action, account, destination and command.
- Confirm that the request matches what you intended the agent to do.
- Approve only the narrow operation needed, or reject it and revise the request.
- If no prompt appears, check whether the product silently blocks the action under a safety policy; a safety block may not produce an approval dialog.
Visual Studio Code documents the distinction plainly: “Approvals determine whether an action runs automatically or requires your confirmation.” An approval prompt therefore does not prove that the command will be allowed to access every path or host.
Evaluate the effective sandbox policy
Find the policy for the machine that executes commands. Check permitted working directories, read-only versus writable paths, child-process restrictions, environment-variable filtering and outbound network rules. A command can be approved and still receive “operation not permitted,” fail to create a file outside the workspace, or be unable to contact a package registry.
Grant only the access required through the product’s supported controls. Avoid disabling the sandbox globally as a first response: broad access can expose source code, credentials and unrelated files, and it obscures which rule caused the failure.
How do I diagnose an MCP server that is unavailable?
Use the harness’s status view and server output, then fix the reported configuration or connection issue before retrying. A server that cannot start is a different problem from a healthy server whose tool the model does not select.
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- Open the Command Palette and run MCP: List Servers.
- Select the affected server and inspect its status.
- Choose Show Output and read the startup, authentication and transport errors.
- Correct the named configuration, executable path, environment variable, endpoint, credential or connection setting.
- Restart the server from the same MCP view, then retry the smallest representative action.
Examples of useful evidence include an executable-not-found message, invalid JSON configuration, an expired credential, a refused port, a certificate failure or a provider response naming a missing scope. Fix the specific condition rather than replacing every configuration file.
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Other coding-agent harnesses
Use the equivalent integration panel, status command or diagnostic log for your product. Google’s coding-agent setup guidance gives examples such as codex mcp list, and points users to the relevant editor extension and output views. Command names change by harness and release, so use the exact command exposed by the installed version.
What if the server is healthy but no tool call appears?
Check the model’s tool-selection and invocation diagnostics. Verify that the tool is exposed to the current conversation, that the selected model can call it, and that the request clearly requires the capability. A running server with no invocation is not evidence of a broken installation; follow the harness-specific “tool not invoked” route and inspect the model response, available-tool list and conversation policy.
Could the network or execution host be the real cause?
Identify where the command and server actually run. In a remote development session, the editor may be on your laptop while the agent, MCP process and shell run in a container, virtual machine or hosted worker. Certificates, proxies, DNS, VPN routes, package caches and firewall rules must be checked on that execution host.
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Trace the failed destination
- Record the hostname, port and protocol named in the error or server output.
- Check DNS resolution and certificate validity from the execution machine.
- Verify proxy variables and organization egress rules for that host.
- Confirm that the required provider endpoint is reachable from the sandbox, not merely from your browser.
- Check whether sign-in redirects or device authorization are blocked in a headless session.
Shell network access can be separate from hosted web search or another built-in agent tool. Success in one channel does not establish permission in another. Do not widen outbound access globally until you know the destination and policy that failed.
Account for dependency and startup failures
A server can fail before it makes a network request if its runtime, package, certificate bundle or executable is missing on the remote host. Compare the environment used to launch the server with the one in which you tested it interactively: operating-system user, working directory, PATH, proxy variables and secret injection often differ.
When should I restart the server, terminal or editor?
Restart after correcting the underlying configuration or connection issue, not as a substitute for diagnosis.
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- Save the corrected server configuration or permission change.
- Stop and restart the MCP server so it reloads endpoints, credentials and environment variables.
- If tools or skills are loaded only at startup, restart the terminal, editor or agent session as well.
- Reconnect the provider only when the authorization record itself was corrected or expired.
- Retry a minimal action, such as listing one resource or reading one test file, before attempting a destructive or multi-step operation.
Repeated reinstalling is unhelpful when the feature is unavailable on the current plan, model, region or workspace. It can also erase useful logs and introduce a second configuration problem.
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Use the evidence and control owner to select the smallest remedy. The table prevents an installation problem from being confused with an authorization, policy or model-invocation problem.
| Failure layer | Evidence to collect | Likely control owner | Appropriate remedy |
|---|---|---|---|
| Availability | Feature list, plan, region, workspace and model | Provider or workspace administrator | Enable the feature, change to a supported surface, or use an available capability |
| Authorization | Account, organization, scopes and provider error | Provider administrator or resource owner | Grant the narrow required permission or reauthorize the correct identity |
| Approval | Pending request and requested destination | User or workspace policy owner | Approve the specific operation or revise the request |
| Sandbox | Effective filesystem and network policy on the execution host | Product or workspace administrator | Allow only the needed path, process or destination |
| Network and host | Endpoint, DNS, proxy, certificate and remote-host diagnostics | Host or network administrator | Repair dependency, route, certificate or proxy configuration |
| MCP server | Server status and Show Output or equivalent logs | User, provider or host administrator | Correct configuration, restart the server and retry |
| Model invocation | Available-tool list, conversation trace and model response | Harness or model configuration owner | Use the invocation diagnostic, adjust the request or select a compatible model |
What should I do when a file, tool or expected step is missing from the response?
Separate an execution failure from an incomplete plan. Ask whether the agent actually attempted the operation, whether the tool returned an error, and whether the requested path or output was within the tool’s scope.
If a file is missing
- Confirm the path is inside an allowed workspace and uses the correct case and separator.
- Check whether the agent ran in a different checkout, container or branch.
- Look for an ignored, generated or unmounted file.
- Ask the agent to list the directory or report its working directory before requesting an edit.
If an expected tool step is missing
Inspect the conversation’s available-tool list and invocation trace. State the required operation and its target explicitly, but do not force a tool call when the integration lacks that capability. If the server is healthy and the model still skips it, use the harness’s tool-invocation diagnostic rather than reinstalling.
If the action stopped halfway
Review the last successful tool result and the first failure. A later step may depend on an output, token, file or approval that was never produced. Resume from the failed dependency instead of rerunning destructive earlier steps.
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- Agent, editor or harness name and version.
- Operating system, execution environment and whether the session is remote.
- Workspace or organization context, without credentials.
- Exact reproduction steps, expected result and actual result.
- Full error text, timestamp and affected tool or server.
- Server status, relevant output and network diagnostics.
- Changes already made and the smallest action that still fails.
Review logs before sharing. Debug exports can contain prompts, source code, local paths, tool inputs and outputs, environment details and other sensitive content. Remove access tokens, cookies, private keys, customer data and confidential code. If an administrator must inspect the raw logs, use the organization’s approved secure channel.
What preventive checks reduce repeat failures?
Keep a short runbook for each agent and integration so that a future failure can be classified quickly.
- Record which account, workspace, model and execution host are expected.
- Document the server’s supported actions and required provider scopes.
- Keep the effective sandbox paths and network destinations narrow and explicit.
- Know where the harness exposes server status, output and invocation traces.
- Test a read-only operation after configuration changes before attempting writes or deployments.
- Track version changes because commands, labels and settings are harness-specific and can change.
- Preserve a sanitized example of a known-good configuration and a known-good server output.
This approach makes the next incident a bounded investigation: establish availability, authorization, approval, policy, host connectivity, server health and invocation in that order.
Frequently Asked Questions
Why can an AI coding agent read a repository but not edit it?
Reading and writing usually use different provider scopes or workspace policies. The account may have read-only repository access, the branch may be protected, or the sandbox may allow reads only. Check the provider role, target branch and effective writable paths separately.
Why does approving a shell command still result in “permission denied”?
Approval controls whether the command may run; it does not expand the command’s sandbox. The process can remain unable to write outside permitted directories, create child processes or reach a blocked network destination. Inspect the policy on the host that executes the command.
Why does an MCP server show as running while the agent never uses it?
A healthy server only proves that its process and transport are available. The current model or conversation may not expose the tool, the request may not trigger tool selection, or harness policy may suppress invocation. Check the available-tool list and invocation trace instead of reinstalling the server.
What information should I give an administrator when an agent fails remotely?
Provide the harness and version, operating system, execution-host details, exact reproduction, full error, server output, endpoint and relevant policy result. State whether the editor and command runner are on different machines, and sanitize prompts, source code, paths, tokens and customer data before sharing logs.
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