feat(agent): conservative automatic node growth for discovery import

[simonperegrinvs]

Summary

• add conservative automatic node growth to discovery import, including parent selection, confidence scoring, duplicate guards, and governance gate enforcement
• keep reference import behavior intact while reporting node outcomes (nodesProposed, nodesCreated, nodeDuplicates, nodeRejected, nodeDetails, skipReasons)
• wire new CLI controls for both agent discovery ingest --auto-import and agent discovery import
• enable auto node growth in run-agent.sh only for real runs (RUN_MODE=real), with conservative defaults
• update docs in CLI.md and README.md

Key Behavior Changes

• imported discovery candidates can now create new nodes + implication edges when:
  • node growth is enabled
  • confidence passes conservative threshold
  • duplicate checks pass
  • governance publish gate allows creation
• weak or missing scope uses fallback signals with stricter confidence requirements
• zero-node runs remain successful but return structured skip reasons

CLI Additions

• --auto-node-growth
• --max-new-nodes <n>
• --min-node-confidence <n>
• --node-review-status <status>
• --node-similarity-threshold <n>

Script Behavior

• run-agent.sh now supports RUN_MODE=real|smoke
• node growth flags are applied only in RUN_MODE=real

Tests

• added/extended behavioral tests in src/agent/__tests__/discovery-import.test.ts for:
  • node creation success
  • low-confidence fallback skip
  • duplicate blocking
  • governance rejection
• added CLI integration coverage in src/cli/commands/__tests__/agent-discovery-import-cli.test.ts
• full suite pass: npm test (123 tests)

Validation

• npm test passed
• npm run lint passed with 2 pre-existing react-hooks warnings unrelated to this PR