docs: update automatic migration compatibility notes

[clockwork-labs-bot]

Summary

• Update automatic migration docs to reflect empty-table removal behavior.
• Document accessor/source-name metadata changes and index accessor rename limits.
• Add a public MCP reference covering spacetime mcp, host-wide vs database-scoped tool shapes, permissions, and common errors.

Audit notes

• Baseline: existing open bot/docs-audit PR docs: update automatic migration compatibility notes #5723; merged current origin/master into bot/docs-audit before adding today's audit fix.
• Commit-impact pass checked new master commits f204baf83 (docs release publishing flow) and 6f37e3ecf (smoketest sharding). No additional public-doc drift found from those commits.
• Skills checked against public docs: CLI, concepts, C#/Rust/TypeScript/C++ server, C#/TypeScript/Unity/Unreal clients, MCP.
• Found MCP operational guidance present in skills/mcp/SKILL.md and current CLI/API code, but missing from public docs beyond the generated CLI command listing.

Validation

• pnpm build