Bug: specify init creates .github in subfolder, breaking Copilot CLI agent discovery

[niksacdev]

Bug Description

When running specify init <directory_name>, the .github folder is created inside the specified directory instead of at the repository root, causing GitHub Copilot CLI to not detect custom agents.

Steps to Reproduce

1. Run specify init
2. The command creates a hve-demo-1/ folder with this structure:

   hve-demo-1/
   ├── .git/
   ├── .github/
   │   ├── agents/
   │   └── prompts/
   ├── .specify/
   └── .vscode/
   

3. Open the directory in VS Code with GitHub Copilot CLI
4. Custom agents are not visible in Copilot CLI (only default Agent, Plan, Ask, Edit appear)

Expected Behavior

The .github/ folder should be created at the repository root level or GitHub Copilot CLI should be able to discover the custom agents, regardless of whether specify init is run.

Actual Behavior

• .github/ is created inside hve-demo-1/ subdirectory
• GitHub Copilot CLI only looks for agents at <repo-root>/.github/agents/
• Custom spec-kit agents are not discovered
• Manual fix required: mv hve-demo-1/.github .

Environment

• OS: macOS
• Tool: GitHub Copilot CLI
• spec-kit version: latest from git

Related Issues

Seems similar to #125, #173, and #790 but specifically about .github placement when using specify init <directory> syntax.

[nicoasdd]

i think you should use specify init . or specify init --here