ingest: scaffold mcp/ alongside toolkit.yaml so 'validate' passes

[tonymenzo]

Problem

scitoolkit ingest writes toolkit.yaml but doesn't scaffold the
mcp/ directory. scitoolkit validate requires mcp/__init__.py
and mcp/server_stdio.py to exist
(scitoolkit/validation.py:469-479), so the next step printed by
ingest's own summary —

Next steps:
  - Edit toolkit.yaml metadata ...
  - Run scitoolkit validate.

— is misleading: validate fails out of the box on a freshly-ingested
toolkit. The author has to know to copy mcp/ from somewhere
(typically a toolkit they previously created with scitoolkit init).

Evidence the gap is known

tests/e2e/run_ingest_e2e.py:144-148 papers over it explicitly:

# mcp/ dir scaffolded to satisfy the existing validation check.
(repo / "mcp").mkdir(exist_ok=True)
(repo / "mcp" / "__init__.py").write_text("", encoding="utf-8")
(repo / "mcp" / "server_stdio.py").write_text("", encoding="utf-8")

Note the e2e writes empty files just to clear the validation check.
That's not a real MCP server — it's a workaround that masks the gap.

Suggested fix

scitoolkit init already does the right thing in
scitoolkit/toolkit.py:196-205: it renders
scitoolkit/templates/mcp/__init__.py.template and
scitoolkit/templates/mcp/server_stdio.py.template with the toolkit's
name/version/description. Extract that block into a small helper —
e.g. _scaffold_mcp_dir(toolkit_path, substitutions) — and call it
from both init and ingest.

For ingest specifically:

• Pull name / version / description from the existing
  toolkit.yaml (so the rendered server_stdio.py uses real values, not
  placeholders). If those keys are still TODO placeholders, render with
  the placeholders unchanged — author will edit them anyway.
• Skip writing if mcp/server_stdio.py already exists, so re-running
  ingest doesn't clobber a customized server. (Match the
  refuse-to-overwrite shape ingest already uses for toolkit.yaml.)
• Mention the scaffolded files in the Next-steps summary so the user
  knows new files appeared.

Relevant files

• scitoolkit/ingest.py — ingest() entry point, currently yaml-only
• scitoolkit/toolkit.py:196-205 — mcp scaffolding to extract
• scitoolkit/templates/mcp/*.template — the templates themselves
• scitoolkit/validation.py:469-479 — what validate checks for
• scitoolkit/cli.py:556-667 — ingest command + Next-steps text
• tests/e2e/run_ingest_e2e.py:144-148 — workaround that should
  delete itself once this is fixed

Related

#1 (silent-drop warning for unresolvable module paths) — separate
issue, also surfaced while onboarding heptapod.