diff --git a/eval/eval.ts b/eval/eval.ts
index b34db2f5..8721deb8 100644
--- a/eval/eval.ts
+++ b/eval/eval.ts
@@ -2,6 +2,7 @@ import * as p from '@clack/prompts';
 import { claudeCodeCli } from './lib/agents/claude-code-cli.ts';
 import * as path from 'node:path';
 import * as fs from 'node:fs/promises';
+import { pathToFileURL } from 'node:url';
 import type { ExperimentArgs } from './types.ts';
 import { prepareExperiment } from './lib/prepare-experiment.ts';
 import { evaluate } from './lib/evaluations/evaluate.ts';
@@ -75,7 +76,7 @@ const experimentArgs: ExperimentArgs = {
 	evalName: args.eval,
 	context: args.context,
 	agent: args.agent,
-	hooks: await import(path.join(evalPath, 'hooks.ts'))
+	hooks: await import(pathToFileURL(path.join(evalPath, 'hooks.ts')).href)
 		.then((mod) => mod.default)
 		.catch(() => ({})),
 };
diff --git a/eval/lib/agents/claude-code-cli.ts b/eval/lib/agents/claude-code-cli.ts
index 832ca140..a7b3191a 100644
--- a/eval/lib/agents/claude-code-cli.ts
+++ b/eval/lib/agents/claude-code-cli.ts
@@ -354,7 +354,6 @@ export const claudeCodeCli: Agent = {
 			'--dangerously-skip-permissions',
 			'--output-format=stream-json',
 			'--verbose',
-			prompt,
 		];
 
 		if (mcpServerConfig) {
@@ -364,12 +363,15 @@ export const claudeCodeCli: Agent = {
 		const claudeProcess = x('claude', args, {
 			nodeOptions: {
 				cwd: projectPath,
-				stdio: ['pipe', 'pipe', 'pipe'], // pipe stdin to send "yes" for MCP prompts
+				stdio: ['pipe', 'pipe', 'pipe'], // pipe stdin to send prompt and "yes" for MCP prompts
 			},
 		});
 		// Auto-approve MCP server trust prompt by sending "1" (Yes, proceed)
+		// Then send the prompt through stdin
 		if (claudeProcess.process?.stdin) {
 			claudeProcess.process?.stdin.write('1\n');
+			claudeProcess.process?.stdin.write(prompt);
+			claudeProcess.process?.stdin.write('\n');
 			claudeProcess.process?.stdin.end();
 		}
 		const messages: ClaudeCodeStreamMessage[] = [];
diff --git a/eval/lib/collect-args.ts b/eval/lib/collect-args.ts
index 188bcbbd..4868b241 100644
--- a/eval/lib/collect-args.ts
+++ b/eval/lib/collect-args.ts
@@ -3,6 +3,7 @@ import * as v from 'valibot';
 import * as p from '@clack/prompts';
 import * as path from 'node:path';
 import * as fs from 'node:fs/promises';
+import { pathToFileURL } from 'node:url';
 import {
 	McpServerConfigSchema,
 	type Context,
@@ -65,9 +66,13 @@ export async function collectArgs() {
 							);
 						}
 						return (
-							await import(path.join(EVALS_DIR, parsedEvalPath, filePath), {
-								with: { type: 'json' },
-							})
+							await import(
+								pathToFileURL(path.join(EVALS_DIR, parsedEvalPath, filePath))
+									.href,
+								{
+									with: { type: 'json' },
+								}
+							)
 						).default;
 					}),
 					McpServerConfigSchema,
@@ -209,7 +214,7 @@ export async function collectArgs() {
 					}
 					if (dirent.name.endsWith('.json') && !dirent.name.includes('mcp')) {
 						const { default: manifestContent } = await import(
-							path.join(evalPath, dirent.name),
+							pathToFileURL(path.join(evalPath, dirent.name)).href,
 							{
 								with: { type: 'json' },
 							}
diff --git a/eval/lib/evaluations/prepare-evaluations.ts b/eval/lib/evaluations/prepare-evaluations.ts
index 55218542..e2cdf36b 100644
--- a/eval/lib/evaluations/prepare-evaluations.ts
+++ b/eval/lib/evaluations/prepare-evaluations.ts
@@ -1,5 +1,6 @@
 import * as path from 'node:path';
 import * as fs from 'node:fs/promises';
+import { pathToFileURL } from 'node:url';
 import { addDevDependency } from 'nypm';
 import type { ExperimentArgs } from '../../types.ts';
 
@@ -27,7 +28,7 @@ export async function prepareEvaluations({ projectPath }: ExperimentArgs) {
 	});
 
 	const { default: pkgJson } = await import(
-		path.join(projectPath, 'package.json'),
+		pathToFileURL(path.join(projectPath, 'package.json')).href,
 		{
 			with: { type: 'json' },
 		}
diff --git a/eval/lib/evaluations/test-stories.ts b/eval/lib/evaluations/test-stories.ts
index c128fd2f..3273bbb0 100644
--- a/eval/lib/evaluations/test-stories.ts
+++ b/eval/lib/evaluations/test-stories.ts
@@ -1,5 +1,6 @@
 import * as path from 'node:path';
 import * as fs from 'node:fs/promises';
+import { pathToFileURL } from 'node:url';
 import type { EvaluationSummary, ExperimentArgs } from '../../types';
 import type { JsonTestResults } from 'vitest/reporters';
 import { x } from 'tinyexec';
@@ -37,9 +38,12 @@ export async function testStories({
 	`,
 	);
 
-	const { default: jsonTestResults } = (await import(testResultsPath, {
-		with: { type: 'json' },
-	})) as { default: JsonTestResults };
+	const { default: jsonTestResults } = (await import(
+		pathToFileURL(testResultsPath).href,
+		{
+			with: { type: 'json' },
+		}
+	)) as { default: JsonTestResults };
 
 	// write the file again to pretty-print it
 	await fs.writeFile(testResultsPath, JSON.stringify(jsonTestResults, null, 2));
diff --git a/eval/lib/prepare-experiment.ts b/eval/lib/prepare-experiment.ts
index 838f61d4..39f66f37 100644
--- a/eval/lib/prepare-experiment.ts
+++ b/eval/lib/prepare-experiment.ts
@@ -1,6 +1,7 @@
 import type { ExperimentArgs } from '../types.ts';
 import * as path from 'node:path';
 import * as fs from 'node:fs/promises';
+import { pathToFileURL } from 'node:url';
 import { installDependencies } from 'nypm';
 import { taskLog } from '@clack/prompts';
 import { runHook } from './run-hook.ts';
@@ -26,9 +27,12 @@ export async function prepareExperiment(experimentArgs: ExperimentArgs) {
 	});
 
 	const packageJsonPath = path.join(experimentArgs.projectPath, 'package.json');
-	const { default: packageJson } = await import(packageJsonPath, {
-		with: { type: 'json' },
-	});
+	const { default: packageJson } = await import(
+		pathToFileURL(packageJsonPath).href,
+		{
+			with: { type: 'json' },
+		}
+	);
 	packageJson.name =
 		`@storybook/mcp-eval--${experimentArgs.evalName}--${path.basename(experimentArgs.experimentPath)}`.toLowerCase();
 
diff --git a/eval/lib/save/chromatic.ts b/eval/lib/save/chromatic.ts
index 34261058..2312f7b3 100644
--- a/eval/lib/save/chromatic.ts
+++ b/eval/lib/save/chromatic.ts
@@ -2,6 +2,7 @@ import type { ExperimentArgs } from '../../types.ts';
 import { runScript } from 'nypm';
 import * as fs from 'node:fs/promises';
 import * as path from 'node:path';
+import { pathToFileURL } from 'node:url';
 import { dedent } from 'ts-dedent';
 import { x } from 'tinyexec';
 
@@ -94,9 +95,12 @@ export async function uploadToChromatic(
 		experimentArgs.projectPath,
 		'chromatic-diagnostics.json',
 	);
-	const { default: diagnostics } = (await import(diagnosticsPath, {
-		with: { type: 'json' },
-	})) as { default: ChromaticDiagnostics };
+	const { default: diagnostics } = (await import(
+		pathToFileURL(diagnosticsPath).href,
+		{
+			with: { type: 'json' },
+		}
+	)) as { default: ChromaticDiagnostics };
 
 	return diagnostics.storybookUrl;
 }