Add scoped auto-import flow and automate daily run script

[simonperegrinvs]

Summary

• add scoped filtering to agent discovery import and agent discovery ingest --auto-import
• classify candidates as in-scope-core, in-scope-adjacent, or out-of-scope using include/exclude keywords + node-link score
• reject out-of-scope candidates with explicit decisionReason and audit entries
• expose new CLI controls:
  • --scope-keyword <keywords...>
  • --exclude-keyword <keywords...>
  • --min-scope-score <n>
  • --no-scope-filter
• replace run-agent.sh prompt-driven flow with a deterministic CLI loop using discovery auto-import + scope filtering
• update docs (CLI.md, README.md) and extend behavior tests for scope filtering

Why

Recent auto-import runs could pull noisy/off-topic papers when discovery lanes were broad. This adds a practical safety gate so automation remains useful without constant manual cleanup.

Validation

• npm test (24 files / 117 tests) passes
• npm run build passes
• bash -n run-agent.sh passes
• real flow test on temp graph (mixed query) imported in-scope psi candidates with scope classifications
• real flow test on temp graph (noise query) showed outOfScope rejections (imported: 0, outOfScope: 5)

Notes

• Semantic Scholar intermittently returned retry-limit failures during live testing; OpenAlex lane was used as fallback for deterministic verification.