docs(operate): clarify deployment and tracing setup

[Zxf-xufeng]

Which issue or RFC does this PR close?

N/A

Rationale for this change

Clarify deployment and tracing setup so new and existing Server operators can follow the documentation safely on Linux and macOS.

What changes are included in this PR?

• Clarify personal service loopback constraints, Windows environment-file ownership, configuration references, and strict readiness checks.
• Add Docker/Compose prerequisites and local-only default-secret guidance for Phoenix and Langfuse tracing.
• Add reproducible Scope creation, two-terminal walkthroughs, and guidance for enabling tracing on an existing Server.
• Add optional Phoenix persistent storage and explain stop, restart, and removal behavior.

Are there any user-facing changes?

Documentation only. No API, runtime behavior, or persisted-format changes.

How was this change tested?

• git diff --check
• CI=true pnpm lint
• CI=true pnpm check:links (189 public pages and 253 repository files)
• pytest -q tests/test_server_tracing.py tests/e2e/test_observability.py::test_inference_spans_join_the_operation_trace_only_when_instrumented (15 passed)

AI usage statement

OpenAI Codex was used to review the deployment flows, edit the documentation, and run validation.