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

## 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

```bash
uv tool install specify-cli
specify init myproj --integration claude --script py
cd myproj
specify preset add

# 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](https://peps.python.org/pep-0668/) (`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`:

```python
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.

Start with .specify/scripts/python/common.py and .specify/scripts/bash/common.sh, especially the interpreter-selection path in _python3_command(), then compare it with the CLI entry point and the dependency declaration in pyproject.toml. Reproduce preset manifest composition after a uv tool install or pipx install. Done means both script variants resolve PyYAML in isolated installs without requiring it in the system interpreter.

Do mô hình lập chỉ mục viết ra từ nội dung của issue.