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A practical guide for Linux devs to debug MCP servers: why clients can’t see tools, time out, or hit “method not found,” and how to fix five pitfalls—stdout logging on stdio/JSON‑RPC, broken initialize/capabilities, schema drift, long-running calls without progress, and PATH/permission/dependency gaps—using curl/jq checks, stderr-first logging, preflight scripts, timeouts, and copy‑pasteable shell tests.