Refactor setup config storage into sections

[vsevolod]

Summary

• move GitHub, LLM, and Slack setup data into a dedicated config_sections table
• make setup-stored config the default source of truth with per-section env override flags
• migrate legacy setup credentials into config_sections on first read and expose override state in dashboard settings

New envs with defaults:

• SLACK_CONFIG_OVERRIDE_FROM_ENV=false
• GITHUB_CONFIG_OVERRIDE_FROM_ENV=false
• LLM_CONFIG_OVERRIDE_FROM_ENV=false

You can add it to the .env to keep all as is and use .env override

Verification

• npm run check
• node --test --test-force-exit --import tsx tests/dashboard-pipelines.test.ts