speckit.clarify Agent Requests /root Access Instead of Project Root

[kenuw]

So this may be a fluke but wanted to raise an issue anyway since it regards /root access request by speckit.clarify. Please see the AI summary below. Thx -Ken

Bug Report: speckit.clarify Agent Requests /root Access Instead of Project Root

Environment

• GitHub Copilot CLI Version: 0.0.396
• Operating System: WSL - Ubuntu 24.04
• Project Directory: /home/user/projects/my-project
• Date Encountered: 2026-01-30

Summary

The speckit.clarify agent attempts to execute a prerequisites check script using /root as the working directory instead of the actual project root directory. This triggers a permission prompt that users must reject, though the agent continues to function correctly afterward.

Steps to Reproduce

1. Navigate to a project directory (e.g., /home/user/projects/my-project)
2. Ensure a spec exists at specs/001-feature-name/spec.md
3. Execute the command: /speckit.clarify
4. Provide answers to clarification questions (reached Question 5 in our case)
5. After answering the final question, the agent attempts to run a prerequisites check

Expected Behavior

The agent should execute its prerequisites check script using the actual project root directory:

cd /home/user/projects/my-project && .specify/scripts/bash/check-prerequisites.sh --json --paths-only

Actual Behavior

The agent attempts to execute:

cd /root && .specify/scripts/bash/check-prerequisites.sh --json --paths-only

This results in a permission prompt that requires user intervention:

✗ Speckit.clarify: Complete clarification workflow
 ✗ Run prerequisites check to get feature paths
   $ cd /root && .specify/scripts/bash/check-prerequisites.sh --json --paths-only
   The user rejected this tool call.

Impact

• Severity: Medium
• User Experience: Users must reject the permission prompt, creating confusion and concern about security
• Functionality: Despite the error, the agent completes its work successfully - the spec file was correctly updated with all clarifications
• Workaround: Users can reject the /root access prompt and the agent will still complete the task

Additional Context

The agent successfully completed all clarification tasks:

• Recorded 5 clarification questions and answers
• Updated the spec file (specs/001-feature-name/spec.md) with appropriate changes
• Removed implementation-specific references and made the spec more technology-agnostic

The error only occurred during what appears to be a final cleanup or validation step.

Related Environment Details

Session Context:

• Session folder: /home/user/.copilot/session-state/<session-uuid>
• Git repository root: /home/user/projects/my-project
• Current working directory: /home/user/projects/my-project

Suggested Fix

The agent should use the detected git repository root or current working directory instead of hardcoded /root path. The project root detection logic should respect the environment context that Copilot CLI already establishes:

# Current (incorrect)
cd /root && .specify/scripts/bash/check-prerequisites.sh

# Should be
cd $PROJECT_ROOT && .specify/scripts/bash/check-prerequisites.sh
# or
cd $GIT_ROOT && .specify/scripts/bash/check-prerequisites.sh

Logs

Error message when attempting to read session output:

Invalid session ID: speckit.clarify. Please supply a valid session ID to read output from.

<no active sessions>

This suggests the agent subprocess may have terminated after the failed prerequisites check, though the spec modifications were successfully committed.