Fix #20: init infers the stack commands no manifest declares

[kaiomp]

Closes flykit-cc/flow#3

The problem

In a script-style Python repo — venv, requirements.txt, tests/test_*.py, an app.py, no pyproject.toml — /flow:init detected nothing, left every *_cmd blank, and signed off with:

[flow init] Done. Next: edit .flow/config.md to fill in your project commands.

/flow:health reported the same blanks the same way. Every one of those commands was discoverable from the repo in under a minute, so this was homework handed back to the user for a step the agent can finish in one pass.

What changed

scripts/init.js

• Detects from evidence that isn't a manifest: requirements*.txt dependencies (pytest, ruff, flake8, mypy, black), Makefile targets, and manage.py. A manifest command still wins over the Makefile wrapper around it.
• Prefers the project's own venv copy of a tool — .venv/bin/pytest, not a bare pytest resolved against whatever is on PATH.
• Ends by naming the keys that are still blank, read back from config.md, so a re-run against an already-initialised project reports its real state rather than a fresh detection. The wording is addressed to the agent: infer each one, verify it runs, write it in. The "edit config.md yourself" line is gone.

commands/init.md — new Step 3, "Fill in what detection missed": work each blank key out from the repo, verify by running it, write it with Edit. Steps renumbered; Edit/Glob/Grep added to allowed-tools.

commands/health.md — a blank *_cmd is now filled in and reported as FIXED, not read back to the user. Health stays diagnostic in every other respect, and the doc says so.

references/stack-command-inference.md (new) — the shared procedure both commands follow: where the evidence for each key lives, preferring the project's environment, how to verify each command without leaving a dev server running, and when a blank is a real decision.

Docs (README.md, SETUP.md, references/config-template.md) no longer tell users to fill blanks in by hand.

Version bumped 0.6.0 -> 0.7.0 across plugin.json, package.json, and marketplace.json.

Testing

$ cd plugins/flow && npm test
ℹ tests 188   ℹ pass 188   ℹ fail 0

$ cd plugins/steuer && npm test
ℹ tests 109   ℹ pass 109   ℹ fail 0

$ ./scripts/check-plugin-versions.sh --since main
ok    flow: bumped 0.6.0 -> 0.7.0

$ find plugins -name '*.js' -not -path '*/node_modules/*' | xargs -n1 node --check
38 scripts, clean

15 new tests cover the requirements/venv/Makefile/manage.py detection, readStackCommands / missingStackCommands, and the closing report — including an assertion that the output never tells the user to edit .flow/config.md.

End-to-end on the repro shape (venv + requirements.txt with pytest + tests/test_app.py + app.py, no pyproject.toml):

  detected: test_cmd = .venv/bin/pytest

[flow init] Done. Stack commands still blank: dev_cmd, lint_cmd, typecheck_cmd, build_cmd, format_cmd
  These are for the agent to finish, not the user. ...