[Bug]: speckit install creates manifest with empty files — no skills available

[rowens-an]

Bug Description

After running specify init --ai claude, the manifest file is created at .specify/integrations/speckit.manifest.json but the files field is empty ({}). No skill files are generated in .claude/commands/, so skills like /speckit-constitution are not recognized by Claude Code.

This is related to but distinct from #1983 — that issue covers missing CLAUDE.md, while this issue is about the skill files themselves not being created.

Steps to Reproduce

1. Run specify init <project> --ai claude
2. Inspect .specify/integrations/speckit.manifest.json
3. Try to invoke /speckit-constitution in Claude Code

Manifest Contents

{
  "integration": "speckit",
  "version": "0.5.0",
  "installed_at": "2026-04-06T19:40:24.619670+00:00",
  "files": {}
}

Expected Behavior

The manifest files field should reference generated skill files, and those files should exist (e.g., .claude/commands/speckit-constitution.md), making /speckit-constitution and other speckit skills available in Claude Code.

Actual Behavior

• .specify/integrations/speckit.manifest.json exists but files is {}
• .claude/commands/ directory does not exist
• /speckit-constitution and other speckit skills are not recognized

Specify CLI Version

0.5.0

AI Agent

Claude Code

Operating System

macOS (Darwin 25.4.0)

[mnriem]

I am unable to reproduce the issue.

Can you please tell me:

1. Does .specify/integrations/claude.manifest.json exist alongside speckit.manifest.json? If so, what are its contents?
2. What does ls -la .claude/skills/ show?
3. How was specify-cli installed — uv tool install, pip install, uvx, or from source?
4. Was this a fresh directory, or had specify init been run previously?
5. Can you retry with a clean cache? uv cache clean && uv tool install specify-cli --force --from git+https://github.com/github/spec-kit.git@v0.5.0