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Agent Skills allowed-tools frontmatter specs not respected in non-interactive mode #3699

Description

@joellis13

Describe the bug

GIVEN any generic skill like:

---
name: greet-user
description: use when a user offers a greeting
allowed-tools:
  - bash
  - shell
  - powershell
  - any-other-tool
---

Run the `./scripts/greet.sh`
<!-- (or `./scripts/greet.py`, `./scripts/greet.bat`, `./scripts/greet.ps1`, etc.) -->

WHEN I prompt with "hello" in interactive mode in Copilot
THEN It works as expected and the script runs, but
WHEN I prompt with "hello" in NON-interactive mode (e.g. copilot -p "hello")
THEN I get a ton of Permission denied and could not request permission from user
AND A ton of wasted tokens, time, and money

Affected version

1.0.60

Steps to reproduce the behavior

All in the above description.

Expected behavior

If a tool is marked as allowed, IT SHOULD BE ALLOWED.

Additional context

No response

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    area:non-interactiveNon-interactive mode (-p), CI/CD, ACP protocol, and headless automationarea:permissionsTool approval, security boundaries, sandbox mode, and directory restrictionsarea:pluginsPlugin system, marketplace, hooks, skills, extensions, and custom agents

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