Harden similarity scoring and entity lifecycle

[stevesolun]

Summary

• validate graph edge score drift, including nested edge objects and score component sums
• align incremental attach with the graph build floor so added nodes draw recommendation edges consistently
• route semantic recommendation cache correctly for custom wiki roots
• pin GitHub raw fallback hydration to branch commit SHAs
• exclude secret-like files from backup snapshot manifests and copies
• reconcile MCP install manifests on skipped/forced installs and manifest-loaded uninstall
• reject protocol-relative links in dashboard wiki rendering
• refresh README/docs test counts after new coverage

Validation

• python scripts\ci_preflight.py --profile pr
• python -m pytest -q --no-cov src\tests\test_import_skills_sh_catalog.py src\tests\test_validate_graph_artifacts.py src\tests\test_recommendation_surfaces_golden.py src\tests\test_incremental_attach_calibration.py src\tests\test_wiki_queue_worker.py src\tests\test_incremental_attach_az_flow.py src\tests\test_vector_index.py src\tests\test_edge_scoring.py src\tests\test_backup_mirror.py src\tests\test_mcp_install.py src\tests\test_install_utils.py
• python -m pytest -q --no-cov src\tests\test_ctx_monitor.py::test_render_wiki_entity_renders_markdown_and_wikilinks src\tests\test_ctx_monitor.py::test_render_mcp_wiki_entity_has_tabs_subgraph_and_quality src\tests\test_ctx_monitor.py::test_render_docs_lists_repo_docs
• python src\validate_graph_artifacts.py --graph-dir graph --deep
• python src\update_repo_stats.py --check