fix(copilot): use --yolo to grant all permissions in non-interactive mode

[mnriem]

Summary

Fixes #2294

The Copilot CLI's --allow-all-tools flag only covers tool execution permissions but does not grant path or URL access. When the Copilot agent autonomously runs shell commands (e.g. npm run build) during workflow execution, the CLI blocks path access and cannot prompt for approval in non-interactive mode, producing:

Permission denied and could not request permission from user

Changes

• Replace --allow-all-tools with --yolo (equivalent to --allow-all-tools --allow-all-paths --allow-all-urls) in both build_exec_args() and dispatch_command() to grant all three permission types
• Rename the opt-out env var from SPECKIT_ALLOW_ALL_TOOLS to SPECKIT_COPILOT_ALLOW_ALL_TOOLS and scope it to the Copilot integration
• Deprecate the old SPECKIT_ALLOW_ALL_TOOLS env var with a UserWarning fallback so existing opt-outs are not silently ignored
• New env var takes precedence when both are set
• Use monkeypatch in tests to avoid flakiness from ambient env vars
• Add tests for deprecation warning, precedence, and opt-out paths

Files changed

• src/specify_cli/integrations/copilot/__init__.py — flag, env var, and deprecation logic
• tests/test_workflows.py — test assertion updates and new env var tests

Testing

All 141 tests pass (workflow + copilot integration suites).

[Copilot]

Pull request overview

This PR updates the GitHub Copilot CLI integration so non-interactive workflow execution can proceed without permission prompts by granting broader Copilot CLI permissions.

Changes:

• Switch Copilot CLI permission flag from --allow-all-tools to --yolo in exec/dispatch paths.
• Rename the opt-out environment variable to SPECKIT_COPILOT_ALLOW_ALL.
• Update workflow test assertion to expect the new flag.

Show a summary per file

File	Description
src/specify_cli/integrations/copilot/init.py	Uses --yolo and a new env var to control “allow all” behavior for Copilot CLI runs.
tests/test_workflows.py	Updates Copilot exec-args assertion to match the new flag.

Copilot's findings

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src/specify_cli/integrations/copilot/init.py:101

• Same env var backwards-compat concern here as in build_exec_args(): removing SPECKIT_ALLOW_ALL_TOOLS means existing opt-out configurations won’t be applied during workflow dispatch, potentially enabling broader permissions than expected. Recommend checking both env vars (with clear precedence) so prior configurations continue to work.

        cli_args = [
            "copilot", "-p", prompt,
            "--agent", agent_name,
        ]
        if os.environ.get("SPECKIT_COPILOT_ALLOW_ALL", "1") != "0":
            cli_args.append("--yolo")

• Files reviewed: 2/2 changed files
• Comments generated: 2

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• Files reviewed: 2/2 changed files
• Comments generated: 2

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• Files reviewed: 2/2 changed files
• Comments generated: 0 new