refactor: deprecate standalone mode, managed mode is now default

[thieung]

Summary

• Remove "managed mode" / "standalone mode" distinction across codebase — managed mode is now the only mode
• Streamline onboard process and environment setup for the new default

Changes

Commit 1: Remove managed/standalone mode distinction (23 files)

Go source (internal/):

• Strip // Managed mode: prefix from route registration comments in server.go
• Replace error messages "requires managed mode" → "requires database stores" in delegate_prep.go, handoff_tool.go, team_tool_manager.go
• Update MCP manager comments to remove standalone references in manager.go, bridge_server.go
• Simplify // --- Managed mode: X --- → // --- DB-backed: X --- in all agent method handlers

Documentation (docs/, api-reference.md):

• Remove redundant (managed mode) qualifiers from section headers and inline text
• Rename sections: Managed Mode Wiring → Database Wiring, Managed Mode -- Providers from Database → Providers from Database, etc.
• Replace "In managed mode, ..." phrasing with direct descriptions
• Mark standalone mode references as deprecated or remove them

Commit 2: Streamline onboard process (9 files)

Backend (cmd/, internal/i18n/):

• Simplify onboard wizard for default managed mode flow
• Extract helpers to cmd/onboard_helpers.go
• Update i18n catalogs (en/vi/zh)

Infrastructure (.env.example, docker-entrypoint.sh, prepare-env.sh):

• Update env example and entrypoint for managed mode as default
• Clean up prepare-env script

Test plan

• go build ./... passes
• go vet ./... passes
• Verify onboard wizard works end-to-end
• Verify Docker entrypoint starts correctly