[Bug] Preset composition fails under isolated installs: scripts run on system python3 but PyYAML lives in the CLI venv

Empieza con .specify/scripts/python/common.py y .specify/scripts/bash/common.sh, especialmente con la ruta de selección del intérprete en _python3_command(), y compárala después con el punto de entrada de la CLI y la declaración de dependencias en pyproject.toml. Reproduce la composición del manifiesto del preset después de una uv tool install o pipx install. Se considera completado cuando ambas variantes del script resuelven PyYAML en instalaciones aisladas sin requerirlo en el intérprete del sistema.

Summary

Preset template composition fails with PyYAML is required to resolve preset template composition whenever the CLI is installed the recommended way (uv tool install or pipx), because the automation scripts run under the system python3 while pyyaml lives in the CLI's isolated venv.

The better the installation isolation, the more reliably the bug shows up.

The chain

1. Command skills instruct the agent to run the script, not the CLI. From speckit-plan:

   Run `python3 .specify/scripts/python/setup_plan.py --json` from repo root
   

2. That script reaches common.py, which does import yaml (line 391 in v1.0.4) and raises TemplateResolutionError("PyYAML is required to resolve preset template composition") when a preset.yml manifest exists.
3. pyyaml>=6.0 is declared in pyproject.toml and is correctly installed — but inside the tool venv created by uv tool install / pipx.
4. The script is invoked as bare python3, which resolves to the system interpreter that cannot see that venv.

Reproduction

uv tool install specify-cli
specify init myproj --integration claude --script py
cd myproj
specify preset add <any preset with a preset.yml>

# CLI path — works (runs inside the tool venv):
specify preset resolve plan-template

# Script path — fails (runs under system python3):
python3 .specify/scripts/python/resolve_template.py plan-template --json
# ERROR: PyYAML is required to resolve preset template composition

Same failure with the bash variant (.specify/scripts/bash/resolve-template.sh), since _python3_command() in common.sh only probes python3 on PATH.

Environment

• spec-kit 1.0.4
• macOS 15 (arm64), Homebrew Python 3.14.6
• Reproduced with both uv tool install specify-cli and pipx install specify-cli

Why the usual workarounds don't apply

• --script py doesn't help: the Python variant is invoked by the same bare python3.
• There is no environment variable to point at another interpreter; _python3_command() only checks PATH.
• Installing pyyaml into the system interpreter is refused on Homebrew/Debian Python under PEP 668 (externally-managed-environment). uv pip install --python "$(which python3)" pyyaml is refused for the same reason and suggests a venv — but a venv doesn't help, because the skills invoke bare python3 with no activation.

The only way out today is bypassing PEP 668 (pip install --user --break-system-packages pyyaml), which asks users to disable a safety mechanism to run a documented feature.

Impact

Any project using a preset with a manifest — i.e. any preset that needs append, prepend or wrap, since the manifest-less path is hardcoded to replace:

except ImportError as exc:
    if manifest_path.is_file():
        raise TemplateResolutionError("PyYAML is required ...")
    return (conventional, "replace") if conventional is not None else None

So composition strategies are unavailable precisely for users who installed the CLI in an isolated environment, which is what the docs recommend.

Suggested fixes

Any one of these would close it:

1. Have the scripts resolve the interpreter that ships with spec-kit (record its path at init time, similar to how some tools pin the interpreter into generated hooks) instead of assuming bare python3.
2. Honor an override such as SPECIFY_PYTHON in _python3_command().
3. Vendor a minimal YAML parser for manifest reading, or parse the small, well-known preset.yml schema without the dependency.
4. If none of the above, document the requirement explicitly in the installation guide, since today it surfaces only as a runtime error.

Happy to send a PR for option 2 if that's the direction you'd prefer.