fix: register preset-provided namespaced commands

[wondr-wclabs]

Summary

Fixes #2862.

Preset command registration was treating every speckit.<domain>.<command> name as an extension command override. That made valid preset-provided commands, such as speckit.extendedflow.reviewer, disappear whenever .specify/extensions/<domain>/ did not exist.

This changes the missing-extension guard so it applies only when the preset is actually targeting an extension command:

• the template explicitly declares replaces: speckit.<ext-id>.<command>; or
• the template uses a composition strategy (prepend, append, or wrap) that needs a lower-priority base command.

A default replace command with a three-part name and no replaces entry is now treated as preset-provided and is registered normally. The existing extension-override behavior is preserved by making the override tests explicit through replaces.

Validation

• uv sync --extra test
• uv run python -m pytest tests/test_presets.py -k "extension_command or three_part_preset_command" -q — 6 passed
• uv run python -m pytest tests/test_presets.py -q — 273 passed
• uv run specify --help
• git diff --check
• uv run python -m pytest -q — 3576 passed, 45 skipped

AI assistance disclosure

This PR was developed with AI assistance from Codex/ChatGPT for codebase inspection, implementation, and validation. I reviewed the resulting diff and test output before submitting.