Sync Agent Kit 8e378953 foundation skills

[huangzesen]

Summary

• repin root and packaged .mcp.json to Agent Kit 8e3789539feb0ce79fe112be17465b40f363696d
• sync the Batch 1 foundational PySPEDAS/IDL shared skills into both root skills/ and plugins/spedas-codex/skills/
• update README resource-count guidance for the 30-skill / 64-resource Agent Kit surface

This keeps spedas_codex as a thin runtime wrapper; no Agent Kit science logic is duplicated here.

Validation

• git diff --check
• python scripts/validate_plugin.py
• root python scripts/smoke_mcp_runtime.py --json — OK, 13 tools / 64 resources
• packaged plugins/spedas-codex: python ../../scripts/smoke_mcp_runtime.py --json — OK, 13 tools / 64 resources