docs: clarify Org API Key and PAT choice

[atx-omni]

Summary

• Present Organization API Key or service-user PAT as an explicit operator choice for validation and optional dbt sync, using the existing secrets and inputs.
• Align installation, security, environment, troubleshooting, and Action descriptions; clarify privileges, redaction, and coverage limits.
• Document current PAT user-scope, personal-folder, and history limitations without advertising unimplemented runtime features. Keep the unreleased AI Repair restrictions unchanged.

Validation

• All 8 focused documentation tests pass, including internal file links and credential-guidance regressions.
• git diff --check passes; final consistency review completed.
• No runtime behavior changes. No live-tenant validation was performed.