Add Sima Atlas: sync runtime, UI panel, MCP server, scripts and atlas docs

[neskuchny]

Motivation

• Provide a lightweight Atlas runtime and UI integration to track block lifecycle, sync checks and agent-driven updates.
• Enable deterministic context-packs and agent tooling (Cursor/Claude/MCP) so agents operate from a single source-of-truth under /atlas rules.
• Automate nightly consolidation, ingestion pipeline and parity/smoke checks to keep atlas-derived docs in sync with runtime state.

Description

• Integrates Atlas into the frontend by extending app_v2.jsx with AtlasSchemaPanel, atlas state hooks, sync/transition actions and context-pack export/mark-dead UI flows.
• Adds a browser runtime Sima_ATLAS_CORE implemented in Sima (Remix)/atlas_sync.js that provides loadAtlas, saveAtlas, syncCheck, transitionBlock, buildContextPack, markFileStatus, and helper validators.
• Adds MCP adapter and Cursor hooks configuration via scripts/mcp_atlas_server.mjs, .cursor/mcp.json, scripts/generate_cursor_hooks.mjs, and generated .cursor/hooks.json, plus AGENTS.md/CLAUDE.md agent contracts.
• Adds a large set of atlas content, context-packs, validators, generators and orchestration tooling including scripts/* (ingestion, context pack builder, nightly consolidation, mcp smoke e2e, pipeline helpers), atlas/* docs (graph, blocks, roadmap, reports, context_packs, health), and test harnesses under tests/.

Testing

• Ran the runtime self-test with node tests/atlas_sync.selftest.mjs, which completed successfully (atlas_sync.selftest: OK).
• Executed the MCP smoke e2e node scripts/mcp_smoke_e2e.mjs, which exercised mcp_atlas_server.mjs tool calls and passed (mcp_smoke_e2e: OK).
• Performed nightly consolidation via node scripts/nightly_consolidation.mjs which generated atlas/nightly_report.md showing a full pass of checks (report summary: PASS 15/15).
• Ran production audit node scripts/audit_production_readiness.mjs which produced atlas/production_audit_report.md indicating all configured checks passed (PASS 5/5).

---

Codex Task