diff --git a/scripts/rea.mjs b/scripts/rea.mjs
index cb97056f8e..fa956d3293 100755
--- a/scripts/rea.mjs
+++ b/scripts/rea.mjs
@@ -129,7 +129,12 @@ if (!(await compiledRuntimeExists(runtimeFiles))) {
   try {
     // Doctor is the readiness report for this failure. Other commands still stop
     // here so they do not run with an unusable log level.
-    if (configurationError !== undefined && !isDoctorCommand(cliArgs)) {
+    if (
+      configurationError !== undefined &&
+      (isShellCompletion ||
+        builtinArguments.splitIncurBuiltinArguments(cliArgs).command[0] !==
+          "doctor")
+    ) {
       process.stderr.write(`${configurationError}\n`);
       process.exitCode = 1;
     } else if (!outputArguments.ok) {
@@ -236,27 +241,6 @@ if (!(await compiledRuntimeExists(runtimeFiles))) {
     throw dispatchFailure;
 }
 
-/** True when the first positional command is `doctor`, after global output flags. */
-function isDoctorCommand(arguments_) {
-  const valuedFlags = new Set([
-    "--format",
-    "--filter-output",
-    "--token-limit",
-    "--token-offset",
-  ]);
-  for (let index = 0; index < arguments_.length; index += 1) {
-    const argument = arguments_[index];
-    if (argument === "--") return arguments_[index + 1] === "doctor";
-    if (valuedFlags.has(argument)) {
-      index += 1;
-      continue;
-    }
-    if (argument.startsWith("-")) continue;
-    return argument === "doctor";
-  }
-  return false;
-}
-
 /**
  * A reader that closes the pipe early, as `rea ... | head` does, has declined
  * the rest of the output. Stop writing without reporting a failure, and exit
diff --git a/tests/boundary/cli/cliLogLevelConfiguration.test.ts b/tests/boundary/cli/cliLogLevelConfiguration.test.ts
index fb6490091f..9aba657f40 100644
--- a/tests/boundary/cli/cliLogLevelConfiguration.test.ts
+++ b/tests/boundary/cli/cliLogLevelConfiguration.test.ts
@@ -1,6 +1,6 @@
 import { expect } from "vitest";
 
-import { cliTest } from "../../support/cli/cliFixture.js";
+import { cliTest, runFileCli } from "../../support/cli/cliFixture.js";
 
 const invalidLogLevelMessage =
   'REA configuration is invalid: REA_LOG_LEVEL: Invalid option: expected one of "trace"|"debug"|"info"|"warn"|"error"|"fatal"|"silent".\n';
@@ -17,23 +17,28 @@ for (const level of ["loud", "INFO"])
       expect(help.stdout).toBe("");
       expect(help.stderr).toBe(invalidLogLevelMessage);
 
-      const doctor = await cli.run({
+      const doctorInvocation = {
         arguments: ["--json", "doctor", "--provider", "hopper"],
         environment: { REA_LOG_LEVEL: level },
-      });
-      expect(doctor.exitCode, doctor.stderr).toBe(1);
-      expect(doctor.stderr).toBe("");
-      expect(doctor.json).toMatchObject({
-        healthy: false,
-        scope_checks: expect.arrayContaining([
-          expect.objectContaining({
-            name: "runtime-configuration:REA_LOG_LEVEL",
-            ok: false,
-            classification: "config_drift",
-            detail: expect.stringContaining("REA_LOG_LEVEL"),
-          }),
-        ]),
-      });
+      };
+      for (const doctor of [
+        await cli.run(doctorInvocation),
+        await runFileCli(cli, doctorInvocation),
+      ]) {
+        expect(doctor.exitCode, doctor.stderr).toBe(1);
+        expect(doctor.stderr).toBe("");
+        expect(doctor.json).toMatchObject({
+          healthy: false,
+          scope_checks: expect.arrayContaining([
+            expect.objectContaining({
+              name: "runtime-configuration:REA_LOG_LEVEL",
+              ok: false,
+              classification: "config_drift",
+              detail: expect.stringContaining("REA_LOG_LEVEL"),
+            }),
+          ]),
+        });
+      }
 
       const client = await cli.run({
         arguments: ["--json", "doctor", "--client", "codex"],
@@ -58,3 +63,46 @@ for (const level of ["loud", "INFO"])
       });
     },
   );
+
+cliTest(
+  "keeps fresh and shared CLI configuration precedence for doctor-looking data",
+  async ({ cli }) => {
+    for (const arguments_ of [
+      ["--filter-output", "doctor", "providers"],
+      ["providers", "doctor"],
+      ["--format", "", "doctor"],
+      ["--filter-output", "", "doctor"],
+      ["--token-limit", "", "doctor"],
+      ["--token-offset", "", "doctor"],
+      ["--unknown", "doctor"],
+      ["--version", "doctor"],
+      ["--", "doctor"],
+    ]) {
+      const invocation = {
+        arguments: arguments_,
+        environment: { REA_LOG_LEVEL: "loud" },
+      };
+      const fresh = await cli.run(invocation);
+      const shared = await runFileCli(cli, invocation);
+      for (const result of [fresh, shared]) {
+        expect(result.exitCode, JSON.stringify(arguments_)).toBe(1);
+        expect(result.stdout, JSON.stringify(arguments_)).toBe("");
+        expect(result.stderr, JSON.stringify(arguments_)).toBe(
+          invalidLogLevelMessage,
+        );
+      }
+    }
+
+    const completion = {
+      arguments: ["doctor"],
+      environment: { REA_LOG_LEVEL: "loud", COMPLETE: "bash" },
+    };
+    const fresh = await cli.run(completion);
+    const shared = await runFileCli(cli, completion);
+    for (const result of [fresh, shared]) {
+      expect(result.exitCode).toBe(1);
+      expect(result.stdout).toBe("");
+      expect(result.stderr).toBe(invalidLogLevelMessage);
+    }
+  },
+);
diff --git a/tests/boundary/cli/dispatcher.test.ts b/tests/boundary/cli/dispatcher.test.ts
index 93e4dba95c..16b7205361 100644
--- a/tests/boundary/cli/dispatcher.test.ts
+++ b/tests/boundary/cli/dispatcher.test.ts
@@ -94,6 +94,96 @@ describe("version report dispatch", () => {
   );
 });
 
+describe("doctor configuration dispatch", () => {
+  workspaceCliTest(
+    "exempts only the production root doctor tokens from invalid logging configuration",
+    async ({ processes, workspace }) => {
+      const imported = "CLI command runtime imported";
+      await installCliRuntime(
+        workspace,
+        `process.stderr.write(${JSON.stringify(`${imported}\n`)}); export const closeCliJavaScriptResources = () => {}; export const createCli = () => ({ serve: (args, options) => options.stdout(JSON.stringify({ adapter: "cli", args })) });\n`,
+      );
+      // Both token ownership and output/configuration admission use production code.
+      await workspace.write(
+        "dist/cli-runtime/cliOutput.js",
+        `export * from ${JSON.stringify(pathToFileURL(resolve("dist/cli-runtime/cliOutput.js")).href)};\n`,
+      );
+      const invoke = (args: readonly string[], completion = "") =>
+        processes.run(
+          process.execPath,
+          [workspace.path("scripts/rea.mjs"), ...args],
+          {
+            cwd: workspace.root,
+            env: {
+              ...process.env,
+              REA_LOG_LEVEL: "invalid-level",
+              COMPLETE: completion,
+            },
+          },
+        );
+
+      for (const [args, normalized] of [
+        [["doctor"], ["doctor"]],
+        [
+          ["--json", "doctor"],
+          ["--json", "doctor"],
+        ],
+        [
+          ["--format=json", "doctor"],
+          ["--format", "json", "doctor"],
+        ],
+        [
+          ["--filter-output", "healthy", "doctor"],
+          ["--filter-output", "healthy", "doctor"],
+        ],
+        [
+          ["--token-limit", "10", "doctor"],
+          ["--token-limit", "10", "doctor"],
+        ],
+        [
+          ["--token-offset", "1", "doctor"],
+          ["--token-offset", "1", "doctor"],
+        ],
+      ] as const) {
+        const result = await invoke(args);
+        expect(
+          result.exitCode,
+          `${JSON.stringify(args)}: ${result.stderr}`,
+        ).toBe(0);
+        expect(result.stderr).toBe(`${imported}\n`);
+        expect(JSON.parse(result.stdout)).toEqual({
+          adapter: "cli",
+          args: normalized,
+        });
+      }
+
+      for (const args of [
+        ["--filter-output", "doctor", "providers"],
+        ["providers", "doctor"],
+        ["--format", "", "doctor"],
+        ["--filter-output", "", "doctor"],
+        ["--token-limit", "", "doctor"],
+        ["--token-offset", "", "doctor"],
+        ["--unknown", "doctor"],
+        ["--version", "doctor"],
+        ["--", "doctor"],
+      ]) {
+        const result = await invoke(args);
+        expect(result.exitCode, JSON.stringify(args)).toBe(1);
+        expect(result.stdout, JSON.stringify(args)).toBe("");
+        expect(result.stderr, JSON.stringify(args)).toContain("REA_LOG_LEVEL");
+        expect(result.stderr, JSON.stringify(args)).not.toContain(imported);
+      }
+
+      const completion = await invoke(["doctor"], "bash");
+      expect(completion.exitCode).toBe(1);
+      expect(completion.stdout).toBe("");
+      expect(completion.stderr).toContain("REA_LOG_LEVEL");
+      expect(completion.stderr).not.toContain(imported);
+    },
+  );
+});
+
 describe("executable dispatcher", () => {
   workspaceCliTest(
     "does not append recovery output after delegated stdout has begun",
diff --git a/tests/support/cli/cliCommandSessionWorker.mjs b/tests/support/cli/cliCommandSessionWorker.mjs
index 54d44b60d3..c98b6aa3ba 100644
--- a/tests/support/cli/cliCommandSessionWorker.mjs
+++ b/tests/support/cli/cliCommandSessionWorker.mjs
@@ -39,6 +39,7 @@ const prepareCliProcess = () => {
 const runtimeFiles = [
   "dist/cli-runtime/cli.js",
   "dist/cli-runtime/cliOutput.js",
+  "dist/cli-runtime/cliBuiltinArguments.js",
   "dist/cli-runtime/cliResultOutput.js",
 ];
 
@@ -54,6 +55,8 @@ const { closeCliJavaScriptResources, createCli } =
   await import("../../../dist/cli-runtime/cli.js");
 const { createCliResultOutput } =
   await import("../../../dist/cli-runtime/cliResultOutput.js");
+const { cliCompletionShell, splitIncurBuiltinArguments } =
+  await import("../../../dist/cli-runtime/cliBuiltinArguments.js");
 const {
   cliConfigurationError,
   normalizeCliArguments,
@@ -161,11 +164,18 @@ async function runOneShot(args) {
   process.exitCode = undefined;
   let explicitExit;
   try {
-    const cliArgs = normalizeCliArguments(args);
-    const outputOptions = parseCliOutputArguments(cliArgs);
+    const isShellCompletion = cliCompletionShell(process.env) !== undefined;
+    const cliArgs = isShellCompletion ? args : normalizeCliArguments(args);
+    const outputOptions = parseCliOutputArguments(
+      isShellCompletion ? [] : cliArgs,
+    );
     const outputArguments = outputOptions.validation;
     const configurationError = cliConfigurationError(process.env);
-    if (configurationError !== undefined && !isDoctorCommand(cliArgs)) {
+    if (
+      configurationError !== undefined &&
+      (isShellCompletion ||
+        splitIncurBuiltinArguments(cliArgs).command[0] !== "doctor")
+    ) {
       process.stderr.write(`${configurationError}\n`);
       process.exitCode = 1;
     } else if (!outputArguments.ok) {
@@ -231,26 +241,6 @@ function captureWrite(chunks) {
   };
 }
 
-function isDoctorCommand(arguments_) {
-  const valuedFlags = new Set([
-    "--format",
-    "--filter-output",
-    "--token-limit",
-    "--token-offset",
-  ]);
-  for (let index = 0; index < arguments_.length; index += 1) {
-    const argument = arguments_[index];
-    if (argument === "--") return arguments_[index + 1] === "doctor";
-    if (valuedFlags.has(argument)) {
-      index += 1;
-      continue;
-    }
-    if (argument.startsWith("-")) continue;
-    return argument === "doctor";
-  }
-  return false;
-}
-
 async function compiledRuntimeExists(paths) {
   for (const path of paths) {
     try {