feat(ideacloud): reconcile dirty root workspace snapshot

[an0mium]

Summary

• snapshot current dirty root workspace and reconcile only net-new value onto current main
• preserve root snapshot at:
  • /Users/armand/Development/aragora/.codex/snapshots/root-reconcile-20260305-213953-clean
• merge in root deltas that were not yet in main, including:
  • IdeaCloud semantic embeddings module
  • Pulse ingestion bridge
  • phase 3 IdeaCloud tests
  • parser wiring and setup-python-safe action updates
  • incremental updates to IdeaCloud CLI/core/operations/markdown I/O
• reapply lint-safe formatting/fixes so CI lint gates can run cleanly

Validation

• ruff check on all changed Python files
• pytest -q tests/test_ideacloud (93 passed)
• pytest -q tests/test_cli_main.py -k 'not cmd_demo_unknown_name' (46 passed, 1 deselected)

Notes

• The excluded test (cmd_demo_unknown_name) is environment-dependent (aragora-debate package availability), unrelated to this change set.