Searches through all indexed documents (PDF, Discord, etc.) and uses RAG
to provide an answer based on retrieved context, with source citations.

Args:
    query: Natural language question to ask.
    document_id: Optional document ID to filter retrieval (from list_documents).
    page_min: Optional start of page range (inclusive). PDF only.
    page_max: Optional end of page range (inclusive). PDF only.
    tag: Optional tag to filter retrieval (from list_documents).
    document_type: Optional type to filter: "pdf", "youtube", "discord", "github", or "plaintext".
    file_path: Optional file path within a document (GitHub: e.g. src/ria/api/atr.c). Use list_documents to see files.
    response_style: Answer style: "thorough" (detailed) or "concise" (default: "thorough").
    ctx: MCP request context (injected by the server; unused).

Returns:
    Dictionary containing answer and sources (document_id, page).

Automatically detects format per path and indexes:
- GitHub (URL, e.g. https://github.com/owner/repo or github.com/owner/repo/tree/branch)
- YouTube (URL or video ID, e.g. https://youtu.be/xyz)
- PDF (.pdf)
- Discord export (.txt with DiscordChatExporter Guild:/Channel: header)

Pass one or more paths. Single path: paths=[\"/path/to/file.pdf\"]. Uses
server config for vector store location and collection. Returns both
successful and failed entries so one bad path does not fail the batch.

Args:
    paths: List of file paths, directory paths, YouTube URLs, or GitHub URLs to index.
    tags: Optional list of tags, one per path (same order as paths).
    branch: For GitHub URLs: override branch (default: main). Ignored for other formats.
    include_patterns: For GitHub URLs: glob patterns for files to include (e.g. ["*.md", "src/**/*.py"]).
    exclude_patterns: For GitHub URLs: glob patterns to exclude. Ignored for other formats.
    ctx: MCP request context (injected by the server; unused).

Returns:
    Dictionary containing indexed entries, failed entries, and totals.

For local files or directories, use add_document_tool instead.

Returns unique document IDs (PDF file names, video IDs, discord-alicia-1200-pcb, owner/repo/path for GitHub, etc.)
currently in the vector store, plus total chunk count. Uses server config
for vector store location and collection.

Args:
    tag: Optional tag to filter: only list documents that have this tag.
    ctx: MCP request context (injected by the server; unused).

Returns:
    Dictionary containing documents, total_chunks, persist_directory,
    collection_name, document_details.

Deletes all chunks and embeddings for the given document. Use
list_documents_tool to see document_ids (e.g. "mybook.pdf", "bwgLXEQdq20", "discord-alicia-1200-pcb", "owner/repo/path" for GitHub).
Uses server config for vector store location and collection.

Args:
    document_id: Document identifier to remove (from list_documents_tool).
    ctx: MCP request context (injected by the server; unused).

Returns:
    Dictionary containing deleted_chunks, document_id, persist_directory, collection_name.