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pipeio_run does not activate cogpy conda env — snakemake not found

Problem

mcp_run in packages/pipeio/src/pipeio/mcp.py:3206 hardcodes snake_cmd = ["snakemake", ...]. But snakemake is installed in the cogpy conda env, not the rag env where the MCP server runs. The bare snakemake command is not on PATH.

Root cause

Same class of bug as the datalad binary resolution issue — tools that shell out to binaries in other conda environments need wrapping with conda run -n <env>.

Fix

  1. mcp_run accepts optional snakemake_cmd: list[str] | None parameter
  2. Projio wrapper resolves snakemake binary from Makefile vars (or known path) with conda wrapping
  3. Same pattern as _resolve_datalad_cmd() in src/projio/mcp/datalad.py