Add batch/pipe mode for CLI tools

## Problem No batch mode available. Users need to either use `--pipe` or chain approach, or use the MCP server directly via stdio with JSON-RPC. ## Proposal Add support for batch processing, options to consider: - `--pipe` flag for stdin/stdout streaming - Chain approach for composing multiple operations - Direct MCP server usage via stdio with JSON-RPC as the primary batch interface ## Context Current CLI tools only support single-operation invocations. For large-scale ontology work (alignment, drift detection, linting across many files), batch processing is essential.