refactor: finish legacy runtime repo cleanup

[maehwasoo]

What

• retarget workspace metadata, label automation, and issue templates from retired packages/mcp / packages/indexer paths to current apps/api ownership
• update plugin advanced settings copy and Python service metadata so current runtime messaging no longer describes the MCP service as a transition layer
• refresh current-state docs and mark historical transition-plan sections as historical record

Why

• PR refactor: complete Python-first local runtime migration #189 removed the legacy runtime implementation, but repo metadata and live docs still referenced the retired Node runtime path
• this follow-up makes the post-migration repo state consistent without rewriting historical records
• Refs feat: plan staged removal of the legacy Node/TypeScript runtime path #181
• Refs feat: complete the later-phase migration to a Python-centered local runtime #179

How

• narrow pnpm-workspace.yaml to the remaining workspace packages and retarget .github/labeler.yml plus issue templates to apps/api
• update apps/api metadata and plugin UI copy to the Python-owned runtime wording
• validate with pnpm install --frozen-lockfile and pnpm check:ci