fix(mcp): avoid startup preference usage signals

[Fail-Safe]

Summary

• Make MCP get_trace usage counting opt-in with record_usage=true.
• Keep startup preference reads out of promotion signals and remove broad startup preference scanning guidance.
• Prevent preference traces from automatic mid-to-long graduation unless manually curated.

Validation

• go test -count=1 ./...
• go test -race ./...
• go vet ./...
• go build ./...
• staticcheck ./...
• make build