perf(mcp): HTTP transport core — add_mcp_http on agent/tool_manager + adata cache + instrumentation

UI exports: fix angle-bracket content loss; embed plots in downloads

UI: save a full-run PDF to the results repo alongside md/json

Fix: raise on MCP tool errors instead of returning error text as a string

Security: replace pickle GPL cache with JSON; document accepted exec risk

Lint cleanup: remove unused imports, empty f-strings, split import lines

Extract _resolve_env_vars from MCPManager.add_mcp (CC 31->26, out of E)

Code-quality fixes: dead assignments, redundant imports, MD5 intent, type hints

HF wheel registry, pinned deps, apt probe, security scan, API-key fallback

Make decoupleR method-limitations text deterministic

Surface exceptions from add_mcp_server's outer try/except in last_discovery_errors

Add handshake timing/timeout diagnostics to MCP discovery

Fix MCP server subprocess using wrong Python interpreter (root cause of 0 tools)

Capture remaining silent zero-tool paths in MCP discovery diagnostics

Capture MCP server subprocess stderr for health-check diagnostics

Surface MCP tool discovery errors in health check

Cap conversation history and code-output size to bound credit cost

Eliminate per-call subprocess overhead with persistent HTTP MCP server

Export Q+A only; save full run to HF with structured sections + clickable link

Remove StateManager class and redundant PlanManager instantiations

Consolidate three tool stores into one (_tool_catalog)

Clean up dead code, fix two bugs, remove unused abstractions

Align project layout with HF Spaces and FastMCP conventions