v0.3.5: mcp-ts-core ^0.12.3 and MCP SDK v2

mcp-ts-core ^0.12.3 and MCP SDK v2

• MCP SDK v2 via @cyanheads/mcp-ts-core ^0.12.3 — HTTP endpoints serve protocol revision 2026-07-28 alongside the 2025 era, and advertised schemas are JSON Schema 2020-12
• Tool arguments are strict — a root-level key a tool does not declare is rejected by name instead of silently stripped
• The advertised outputSchema declares the error envelope, so a client that validates structuredContent without checking isError no longer rejects a typed failure with -32602
• paleobiology_dataframe_drop registers through disabledTool() — still off tools/list, now shown on the HTTP landing page with the env var that enables it
• Bun pins move to 1.4.0; the Docker build stage runs on $BUILDPLATFORM and the production stage installs with --omit=peer
• PBDB_TIMEOUT_MS bounds the whole PBDB exchange, not just the response headers
• Session-mode docs, security contact, typechecked tests, and a framework skills/scripts re-sync
• deps: @cyanheads/mcp-ts-core ^0.11.0 → ^0.12.3 (+ @duckdb/node-api and dev-dep bumps)

CHANGELOG v0.3.5