refactor: complete Python-first local runtime migration

[maehwasoo]

What

• move MCP transport, vault tool execution, and index maintenance into the Python runtime under apps/api
• switch the Obsidian plugin defaults and bundled path resolution to uv run --directory ... apps/api
• remove packages/mcp and packages/indexer, then update release/docs/workflows for the Python-only runtime

Why

• complete the Python-centered local runtime migration tracked by feat: complete the later-phase migration to a Python-centered local runtime #179
• remove the last legacy Node/TypeScript runtime path tracked by feat: plan staged removal of the legacy Node/TypeScript runtime path #181
• Fixes feat: complete the later-phase migration to a Python-centered local runtime #179
• Fixes feat: plan staged removal of the legacy Node/TypeScript runtime path #181

How

• add Python MCP and indexer CLIs plus vault/index/write-tool runtime coverage in apps/api
• add parity and path-resolution tests for the Python-owned runtime path
• validate with pnpm check:ci and the pre-push hook (pnpm check)

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

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