fix: tech-debt: sweep cron-isms from code comments, helpers, lib, and public site copy (#548)

- Rename acquire_cron_lock → acquire_run_lock in lib/formula-session.sh
  and all five *-run.sh call sites
- Update all *-run.sh file headers: "Cron wrapper" → "Polling-loop wrapper"
- Rewrite docs/updating-factory.md: replace crontab check with pgrep,
  replace "Crontab empty after restart" section with polling-loop equivalent
- Update docs/EVAL-MCP-SERVER.md to reflect polling-loop reality
- Update lib/guard.sh, lib/AGENTS.md, lib/ci-setup.sh comments
- Update formulas/*.toml comments (cron → polling loop)
- Update dev/dev-poll.sh usage comment
- Update tests/smoke-init.sh to handle compose vs bare-metal scheduling
- Update .woodpecker/agent-smoke.sh comments
- Update site HTML: architecture.html, quickstart.html, index.html
- Clarify _install_cron_impl is bare-metal only (compose uses polling loop)
- Keep site/collect-engagement.sh and site/collect-metrics.sh cron refs
  (genuinely cron-driven on the website host, separate from factory loop)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

bin/disinto

@@ -506,7 +506,8 @@ copy_issue_templates() {
   done
 }
 
-# Install cron entries for project agents (implementation in lib/ci-setup.sh)
+# Install scheduling entries for project agents (implementation in lib/ci-setup.sh)
+# In compose mode this is a no-op (the agents container uses a polling loop).
 install_cron() {
   _load_ci_context
   _install_cron_impl "$@"
@@ -765,7 +766,7 @@ p.write_text(text)
   # Copy issue templates to target project
   copy_issue_templates "$repo_root"
 
-  # Install cron jobs
+  # Install scheduling (bare-metal: cron; compose: polling loop in entrypoint.sh)
   install_cron "$project_name" "$toml_path" "$auto_yes" "$bare"
 
   # Set up mirror remotes if [mirrors] configured in TOML