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>

lib/ci-setup.sh

@@ -1,9 +1,9 @@
 #!/usr/bin/env bash
 # =============================================================================
-# ci-setup.sh — CI setup functions for Woodpecker and cron configuration
+# ci-setup.sh — CI setup functions for Woodpecker and scheduling configuration
 #
 # Internal functions (called via _load_ci_context + _*_impl):
-#   _install_cron_impl()              - Install crontab entries for project agents
+#   _install_cron_impl()              - Install crontab entries (bare-metal only; compose uses polling loop)
 #   _create_woodpecker_oauth_impl()   - Create OAuth2 app on Forgejo for Woodpecker
 #   _generate_woodpecker_token_impl() - Auto-generate WOODPECKER_TOKEN via OAuth2 flow
 #   _activate_woodpecker_repo_impl()  - Activate repo in Woodpecker
@@ -30,12 +30,13 @@ _load_ci_context() {
   fi
 }
 
-# Generate and optionally install cron entries for the project agents.
+# Generate and optionally install cron entries for bare-metal deployments.
+# In compose mode, the agents container uses a polling loop (entrypoint.sh) instead.
 # Usage: install_cron <name> <toml_path> <auto_yes> <bare>
 _install_cron_impl() {
   local name="$1" toml="$2" auto_yes="$3" bare="${4:-false}"
 
-  # In compose mode, skip host cron — the agents container runs cron internally
+  # In compose mode, skip host cron — the agents container uses a polling loop
   if [ "$bare" = false ]; then
     echo ""
     echo "Cron:    skipped (agents container handles scheduling in compose mode)"