Fix MCP stdio native log pollution

CHANGELOG.md

@@ -10,6 +10,7 @@
   hashes referenced by sibling collections, and drops `vectors_vec` only
   when the scoped clear empties all vectors.
 - Hybrid search: weight RRF lists by query type so original FTS and original vector evidence get the intended 2x boost, instead of accidentally boosting the first lexical expansion. #591
+- MCP: seed llama.cpp/GGML quiet env vars before launching `qmd mcp` so native logs cannot pollute stdio JSON-RPC framing. #593
 - GPU: respect explicit `QMD_LLAMA_GPU=metal|vulkan|cuda` backend overrides instead of always using auto GPU selection. #529
 - Fix: preserve original filename case in `handelize()`. The previous
   `.toLowerCase()` call made indexed paths unreachable on case-sensitive

bin/qmd

@@ -15,6 +15,16 @@ done
 # to avoid native module ABI mismatches (e.g., better-sqlite3 compiled for bun vs node)
 DIR="$(cd -P "$(dirname "$SOURCE")/.." && pwd)"
 
+# MCP stdio reserves stdout exclusively for JSON-RPC frames. node-llama-cpp
+# / llama.cpp / ggml can write native logs directly to stdout before JS-level
+# log handlers are attached, so seed the native quiet env before Node/Bun imports
+# the CLI and its LLM modules. Preserve explicit user values when provided.
+if [ "$1" = "mcp" ]; then
+  export LLAMA_LOG_LEVEL="${LLAMA_LOG_LEVEL:-error}"
+  export GGML_LOG_LEVEL="${GGML_LOG_LEVEL:-error}"
+  export GGML_BACKEND_SILENT="${GGML_BACKEND_SILENT:-1}"
+fi
+
 # Detect the package manager that installed dependencies by checking lockfiles.
 # $BUN_INSTALL is intentionally NOT checked — it only indicates that bun exists
 # on the system, not that it was used to install this package (see #361).

test/cli.test.ts

@@ -6,7 +6,7 @@
  */
 
 import { describe, test, expect, beforeAll, afterAll, beforeEach } from "vitest";
-import { mkdtemp, rm, writeFile, mkdir } from "fs/promises";
+import { chmod, copyFile, mkdtemp, rm, writeFile, mkdir } from "fs/promises";
 import { existsSync, lstatSync, readFileSync, symlinkSync, writeFileSync, unlinkSync } from "fs";
 import { tmpdir } from "os";
 import { join, dirname } from "path";
@@ -1601,3 +1601,67 @@ describe("mcp http daemon", () => {
     try { unlinkSync(pidPath()); } catch {}
   });
 });
+
+// =============================================================================
+// MCP stdio stdout hygiene
+// =============================================================================
+
+describe("mcp stdio launcher", () => {
+  test("sets native llama/ggml quiet env before Node starts so stdout stays JSON-RPC only", async () => {
+    const tempPackage = await mkdtemp(join(tmpdir(), "qmd-bin-mcp-"));
+    try {
+      await mkdir(join(tempPackage, "bin"), { recursive: true });
+      await mkdir(join(tempPackage, "dist", "cli"), { recursive: true });
+      await mkdir(join(tempPackage, "fake-bin"), { recursive: true });
+
+      const qmdBin = join(tempPackage, "bin", "qmd");
+      await copyFile(join(projectRoot, "bin", "qmd"), qmdBin);
+      await chmod(qmdBin, 0o755);
+
+      // Force the wrapper down the Node branch, then put our fake `node` first
+      // in PATH. The fake node behaves like the native llama/ggml layer: it
+      // writes a non-JSON stdout line unless qmd pre-seeded the documented
+      // quiet env vars before launching JS.
+      await writeFile(join(tempPackage, "package-lock.json"), "{}\n");
+      const fakeNode = join(tempPackage, "fake-bin", "node");
+      await writeFile(fakeNode, `#!/bin/sh
+if [ "\${GGML_BACKEND_SILENT:-}" != "1" ]; then
+  printf 'llama.cpp native log on stdout\\n'
+fi
+printf '{"jsonrpc":"2.0","id":1,"result":{"ok":true}}\\n'
+`);
+      await chmod(fakeNode, 0o755);
+
+      const proc = spawn(qmdBin, ["mcp"], {
+        cwd: tempPackage,
+        env: {
+          ...process.env,
+          PATH: `${join(tempPackage, "fake-bin")}:${process.env.PATH}`,
+          LLAMA_LOG_LEVEL: "",
+          GGML_LOG_LEVEL: "",
+          GGML_BACKEND_SILENT: "",
+        },
+        stdio: ["ignore", "pipe", "pipe"],
+      });
+
+      let stdout = "";
+      let stderr = "";
+      proc.stdout?.on("data", (chunk: Buffer) => { stdout += chunk.toString(); });
+      proc.stderr?.on("data", (chunk: Buffer) => { stderr += chunk.toString(); });
+      const exitCode = await new Promise<number>((resolve, reject) => {
+        proc.once("error", reject);
+        proc.on("close", (code) => resolve(code ?? 1));
+      });
+
+      expect(exitCode).toBe(0);
+      expect(stderr).toBe("");
+      const lines = stdout.trim().split("\n").filter(Boolean);
+      expect(lines.length).toBeGreaterThan(0);
+      for (const line of lines) {
+        expect(() => JSON.parse(line)).not.toThrow();
+      }
+    } finally {
+      await rm(tempPackage, { recursive: true, force: true });
+    }
+  });
+});