scaffold_from_template flattens the template tycoon.yml when stamping schema_version

[db-tycoon-stephen]

Found during review of #178 (T2-4).

scaffold_from_template copies the template tycoon.yml with shutil.copy2, which preserves the file verbatim — then immediately undoes that with a yaml.safe_load / yaml.dump round-trip to stamp schema_version:

shutil.copy2(src_yml, dst_yml)
_raw = yaml.safe_load(dst_yml.read_text()) or {}
_raw["schema_version"] = SCHEMA_VERSION
dst_yml.write_text(yaml.dump(_raw, default_flow_style=False, sort_keys=False))

Effect

Verified against src/tycoon/templates/nyc-transit/tycoon.yml:

• 41 lines → 37
• all 5 blank-line section separators stripped, so the file arrives as one dense block
• schema_version appended at line 36, at the bottom, rather than next to version: at the top

This is the first file a new user opens after tycoon init --template.

Why it's inconsistent

migrate_project deliberately uses ruamel.yaml precisely to preserve comments and blank lines. This path throws that away for the same stamping job.

Suggested fix

Drop the manual round-trip and call migrate_project(dst_yml.parent) after the copy. It's ruamel-based, already tested, idempotent, and stamps schema_version plus metadata: defaults in one shot.

scaffold_blank_project is unaffected — it builds the dict itself, so there's no formatting to preserve.

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Mirrored in Jira: PTC-110 (Subtask of PTC-84, [Rewrite M2]). Dev work continues here.