chore(security): stop committing Axis runtime state, lock workspace root private

- Untrack packages/axis-server/.axis-server.log and .axis/instructions/*
  (auto-generated when the server runs from inside the package dir; no
  secrets, but runtime state should never be committed/published).
- Gitignore .axis-server.log and .axis/instructions/ everywhere while
  keeping .axis/axis.json (project config) trackable.
- Mark the workspace root package private:true so `npm publish` can never
  ship the whole repo (no version/bin/files; it is a dev root, not a package).
- Extend package-contents tests to assert root privacy, ignored runtime
  state, and that no log/instructions files are tracked.

Audit also verified: both publishable packages have correct files allowlists,
.env.local/source maps/supabase dumps are all gitignored, and git history
contains no real secrets (the dotenv README RSA placeholder is not in HEAD).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>