fix(security): enforce discovery and analysis completeness

[Spectorian]

Summary

• include bounded dot-prefixed child skills while preserving explicit skip directories and link safeguards
• keep requested and executed optional-analysis state distinct across reports and MCP output
• require a complete requested analysis pass for an install-safe MCP verdict while preserving explicit static-only behavior

Validation

• 276 focused and adversarial regressions
• 2,806 non-integration/non-provider tests
• cross-surface JSON and MCP accounting checks
• Ruff lint, format check, targeted mypy, and git diff --check

[rng1995]

Requesting changes because the requested semantic pass can still be skipped entirely while this PR reports it as used and complete, producing an install-safe verdict. The current-head end-to-end repro executes zero semantic calls but returns llm_used=True, scan_mode=static+llm, recommendation=SAFE, and safe_to_install=True.

[rng1995]

[P1] Do not count an empty call log as a completed LLM pass. If the graph is imported before provider credentials are available, credential-gated semantic nodes are omitted. Binding a supported provider later through use_provider makes preflight succeed, but no semantic nodes or calls run and llm_call_log remains empty. This branch then returns (used=True, complete=True), allowing a SAFE/safe_to_install=True result even though meta_analysis_applied=False. Treat an empty log as not used/incomplete, or retain the expected analyzers and account their explicit statuses before allowing an install approval.