docs: refresh README for PR 19 features

[Coding-Dev-Tools]

Summary

• document every user-facing feature family added in PR Add unified repo graph, intent-native memory, and Pro/Team hardening #19
• expand repository graph, schema-v3 layers, intent-native APIs, receipts, ingestion, retention, and security guidance
• align the README with the current 28-tool MCP surface, including scope promotion
• clarify sync and managed-relay security boundaries

Validation

• PR-focused protocol, graph, resource, receipt, sync, auth, service, and engine tests pass
• local README links resolve
• MCP inventory check confirms 28 tools
• git diff --check passes

Only README.md is included in this PR.