Most write-ups on building an MCP server focus on the protocol itself: defining tools, handling requests, wiring up a client. That part is genuinely straightforward. What gets skipped over far more often is what changes when the tool you are exposing operates on files rather than returning data. File processing introduces a specific set of security and reliability problems that a typical read-only API does not have to think about, and getting them wrong is easy to miss until something goes badly.
This is a rundown of the decisions that mattered most while building an MCP server that exposes document processing tools, merge, convert, OCR, and similar operations, and why a few of the obvious approaches turned out to be the wrong ones.
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