diff --git a/packages/cli/src/cli-program.ts b/packages/cli/src/cli-program.ts
index 8b517a3b..fd7a50ef 100644
--- a/packages/cli/src/cli-program.ts
+++ b/packages/cli/src/cli-program.ts
@@ -179,6 +179,7 @@ async function runBareInteractiveCommand(
         skipAgents: false,
         inputMode: 'auto',
         yes: false,
+        cliVersion: context.packageInfo.version,
         skipLlm: false,
         skipEmbeddings: false,
         databaseSchemas: [],
diff --git a/packages/cli/src/commands/setup-commands.ts b/packages/cli/src/commands/setup-commands.ts
index 1d5a933a..16e3cc28 100644
--- a/packages/cli/src/commands/setup-commands.ts
+++ b/packages/cli/src/commands/setup-commands.ts
@@ -371,6 +371,7 @@ export function registerSetupCommands(program: Command, context: KtxCliCommandCo
       skipAgents: options.skipAgents === true,
       inputMode: options.input === false ? 'disabled' : 'auto',
       yes: options.yes === true,
+      cliVersion: context.packageInfo.version,
       ...(options.anthropicApiKeyEnv ? { anthropicApiKeyEnv: options.anthropicApiKeyEnv } : {}),
       ...(options.anthropicApiKeyFile ? { anthropicApiKeyFile: options.anthropicApiKeyFile } : {}),
       ...(options.anthropicModel ? { anthropicModel: options.anthropicModel } : {}),
diff --git a/packages/cli/src/index.test.ts b/packages/cli/src/index.test.ts
index 4f3a0a59..0e4b4b1a 100644
--- a/packages/cli/src/index.test.ts
+++ b/packages/cli/src/index.test.ts
@@ -324,6 +324,7 @@ describe('runKtxCli', () => {
           skipAgents: false,
           inputMode: 'auto',
           yes: false,
+          cliVersion: '0.0.0-private',
           skipLlm: false,
           skipEmbeddings: false,
           databaseSchemas: [],
@@ -1015,6 +1016,7 @@ describe('runKtxCli', () => {
         command: 'run',
         projectDir: tempDir,
         inputMode: 'disabled',
+        cliVersion: '0.0.0-private',
         anthropicApiKeyEnv: 'ANTHROPIC_API_KEY',
         anthropicModel: 'claude-sonnet-4-6',
         skipLlm: false,
@@ -1122,6 +1124,7 @@ describe('runKtxCli', () => {
         projectDir: '/tmp/project',
         inputMode: 'disabled',
         yes: true,
+        cliVersion: '0.0.0-private',
         skipLlm: true,
         skipEmbeddings: true,
         databaseDrivers: ['postgres'],
diff --git a/packages/cli/src/setup.test.ts b/packages/cli/src/setup.test.ts
index 3e772d92..5901013a 100644
--- a/packages/cli/src/setup.test.ts
+++ b/packages/cli/src/setup.test.ts
@@ -318,6 +318,7 @@ describe('setup status', () => {
           skipAgents: true,
           inputMode: 'disabled',
           yes: true,
+          cliVersion: '0.2.0',
           skipLlm: true,
           skipEmbeddings: true,
           databaseSchemas: [],
@@ -364,6 +365,7 @@ describe('setup status', () => {
           skipAgents: false,
           inputMode: 'auto',
           yes: false,
+          cliVersion: '0.2.0',
           skipLlm: false,
           skipEmbeddings: false,
           databaseSchemas: [],
@@ -410,6 +412,7 @@ describe('setup status', () => {
           skipAgents: false,
           inputMode: 'auto',
           yes: false,
+          cliVersion: '0.2.0',
           skipLlm: false,
           skipEmbeddings: false,
           databaseSchemas: [],
@@ -434,6 +437,7 @@ describe('setup status', () => {
           skipAgents: false,
           inputMode: 'auto',
           yes: false,
+          cliVersion: '0.2.0',
           skipLlm: false,
           skipEmbeddings: false,
           databaseSchemas: [],
@@ -472,6 +476,7 @@ describe('setup status', () => {
           skipAgents: true,
           inputMode: 'auto',
           yes: false,
+          cliVersion: '0.2.0',
           skipLlm: true,
           skipEmbeddings: true,
           databaseSchemas: [],
@@ -530,6 +535,7 @@ describe('setup status', () => {
           skipAgents: true,
           inputMode: 'auto',
           yes: false,
+          cliVersion: '0.2.0',
           skipLlm: true,
           skipEmbeddings: true,
           databaseSchemas: [],
@@ -597,6 +603,7 @@ describe('setup status', () => {
           skipAgents: true,
           inputMode: 'auto',
           yes: false,
+          cliVersion: '0.2.0',
           skipLlm: true,
           skipEmbeddings: true,
           databaseSchemas: [],
@@ -661,6 +668,7 @@ describe('setup status', () => {
           skipAgents: true,
           inputMode: 'auto',
           yes: false,
+          cliVersion: '0.2.0',
           skipLlm: false,
           skipEmbeddings: true,
           databaseSchemas: [],
@@ -697,6 +705,7 @@ describe('setup status', () => {
           skipAgents: false,
           inputMode: 'auto',
           yes: false,
+          cliVersion: '0.2.0',
           skipLlm: false,
           skipEmbeddings: false,
           databaseSchemas: [],
@@ -733,6 +742,7 @@ describe('setup status', () => {
           skipAgents: true,
           inputMode: 'disabled',
           yes: false,
+          cliVersion: '0.2.0',
           skipLlm: true,
           skipEmbeddings: true,
           databaseSchemas: [],
@@ -764,6 +774,7 @@ describe('setup status', () => {
           skipAgents: true,
           inputMode: 'disabled',
           yes: false,
+          cliVersion: '0.2.0',
           skipLlm: true,
           skipEmbeddings: true,
           databaseSchemas: [],
@@ -791,6 +802,7 @@ describe('setup status', () => {
           skipAgents: true,
           inputMode: 'disabled',
           yes: false,
+          cliVersion: '0.2.0',
           skipLlm: false,
           skipEmbeddings: true,
           databaseSchemas: [],
@@ -819,6 +831,7 @@ describe('setup status', () => {
           skipAgents: true,
           inputMode: 'disabled',
           yes: false,
+          cliVersion: '0.2.0',
           anthropicApiKeyEnv: 'ANTHROPIC_API_KEY',
           anthropicModel: 'claude-sonnet-4-6',
           skipLlm: false,
@@ -858,7 +871,8 @@ describe('setup status', () => {
           agents: false,
           skipAgents: true,
           inputMode: 'disabled',
-          yes: false,
+          yes: true,
+          cliVersion: '0.2.0',
           anthropicApiKeyEnv: 'ANTHROPIC_API_KEY',
           anthropicModel: 'claude-sonnet-4-6',
           skipLlm: false,
@@ -878,6 +892,8 @@ describe('setup status', () => {
       expect.objectContaining({
         projectDir: tempDir,
         inputMode: 'disabled',
+        cliVersion: '0.2.0',
+        runtimeInstallPolicy: 'auto',
         embeddingBackend: 'openai',
         embeddingApiKeyEnv: 'OPENAI_API_KEY',
         skipEmbeddings: false,
@@ -886,6 +902,43 @@ describe('setup status', () => {
     );
   });
 
+  it('passes no-input runtime policy to the embeddings step', async () => {
+    const io = makeIo();
+    const embeddings = vi.fn(async () => ({ status: 'failed' as const, projectDir: tempDir }));
+
+    await expect(
+      runKtxSetup(
+        {
+          command: 'run',
+          projectDir: tempDir,
+          mode: 'new',
+          agents: false,
+          agentScope: 'project',
+          agentInstallMode: 'cli',
+          skipAgents: true,
+          inputMode: 'disabled',
+          yes: false,
+          cliVersion: '0.2.0',
+          skipLlm: true,
+          skipEmbeddings: false,
+          databaseSchemas: [],
+          skipDatabases: true,
+          skipSources: true,
+        },
+        io.io,
+        { embeddings },
+      ),
+    ).resolves.toBe(1);
+
+    expect(embeddings).toHaveBeenCalledWith(
+      expect.objectContaining({
+        cliVersion: '0.2.0',
+        runtimeInstallPolicy: 'never',
+      }),
+      io.io,
+    );
+  });
+
   it('lets Back from embedding setup return to the model step instead of exiting', async () => {
     const testIo = makeIo();
     const modelResults = [
@@ -905,6 +958,7 @@ describe('setup status', () => {
           skipAgents: true,
           inputMode: 'auto',
           yes: false,
+          cliVersion: '0.2.0',
           skipLlm: false,
           skipEmbeddings: false,
           databaseSchemas: [],
@@ -952,6 +1006,7 @@ describe('setup status', () => {
           skipAgents: true,
           inputMode: 'auto',
           yes: false,
+          cliVersion: '0.2.0',
           skipLlm: false,
           skipEmbeddings: false,
           databaseSchemas: [],
@@ -997,6 +1052,7 @@ describe('setup status', () => {
           skipAgents: true,
           inputMode: 'auto',
           yes: false,
+          cliVersion: '0.2.0',
           skipLlm: false,
           skipEmbeddings: true,
           databaseSchemas: [],
@@ -1037,6 +1093,7 @@ describe('setup status', () => {
           skipAgents: true,
           inputMode: 'disabled',
           yes: false,
+          cliVersion: '0.2.0',
           anthropicApiKeyEnv: 'ANTHROPIC_API_KEY',
           anthropicModel: 'claude-sonnet-4-6',
           skipLlm: false,
@@ -1084,6 +1141,7 @@ describe('setup status', () => {
           skipAgents: true,
           inputMode: 'disabled',
           yes: true,
+          cliVersion: '0.2.0',
           skipLlm: true,
           skipEmbeddings: true,
           skipDatabases: true,
@@ -1130,6 +1188,7 @@ describe('setup status', () => {
           agents: false,
           inputMode: 'disabled',
           yes: true,
+          cliVersion: '0.2.0',
           skipLlm: true,
           skipEmbeddings: true,
           skipDatabases: true,
@@ -1191,6 +1250,7 @@ describe('setup status', () => {
           agentInstallMode: 'cli',
           inputMode: 'disabled',
           yes: true,
+          cliVersion: '0.2.0',
           skipLlm: true,
           skipEmbeddings: true,
           skipDatabases: true,
@@ -1244,6 +1304,7 @@ describe('setup status', () => {
           agentInstallMode: 'cli',
           inputMode: 'disabled',
           yes: true,
+          cliVersion: '0.2.0',
           skipLlm: true,
           skipEmbeddings: true,
           skipDatabases: true,
@@ -1277,6 +1338,7 @@ describe('setup status', () => {
           agents: false,
           inputMode: 'disabled',
           yes: true,
+          cliVersion: '0.2.0',
           skipLlm: true,
           skipEmbeddings: true,
           skipDatabases: true,
@@ -1375,6 +1437,7 @@ describe('setup status', () => {
           agents: false,
           inputMode: 'auto',
           yes: false,
+          cliVersion: '0.2.0',
           skipLlm: false,
           skipEmbeddings: false,
           skipDatabases: false,
@@ -1437,6 +1500,7 @@ describe('setup status', () => {
           agentInstallMode: 'both',
           inputMode: 'disabled',
           yes: true,
+          cliVersion: '0.2.0',
           skipLlm: false,
           skipEmbeddings: false,
           skipDatabases: false,
@@ -1485,6 +1549,7 @@ describe('setup status', () => {
           skipAgents: true,
           inputMode: 'disabled',
           yes: false,
+          cliVersion: '0.2.0',
           anthropicApiKeyEnv: 'ANTHROPIC_API_KEY',
           anthropicModel: 'claude-sonnet-4-6',
           skipLlm: false,
diff --git a/packages/cli/src/setup.ts b/packages/cli/src/setup.ts
index 09deff37..baf1adeb 100644
--- a/packages/cli/src/setup.ts
+++ b/packages/cli/src/setup.ts
@@ -60,6 +60,7 @@ export type KtxSetupArgs =
       skipAgents?: boolean;
       inputMode: 'auto' | 'disabled';
       yes: boolean;
+      cliVersion: string;
       anthropicApiKeyEnv?: string;
       anthropicApiKeyFile?: string;
       anthropicModel?: string;
@@ -397,6 +398,13 @@ function writeContextNotReadyForAgents(projectDir: string, io: KtxCliIo): void {
   io.stderr.write(`Then install agent integration:\n  ktx setup --agents --project-dir ${resolve(projectDir)}\n`);
 }
 
+function setupRuntimeInstallPolicy(args: Extract<KtxSetupArgs, { command: 'run' }>): 'prompt' | 'auto' | 'never' {
+  if (args.yes) {
+    return 'auto';
+  }
+  return args.inputMode === 'disabled' ? 'never' : 'prompt';
+}
+
 export async function runKtxSetup(args: KtxSetupArgs, io: KtxCliIo, deps: KtxSetupDeps = {}): Promise<number> {
   try {
     return await runKtxSetupInner(args, io, deps);
@@ -566,6 +574,8 @@ async function runKtxSetupInner(args: KtxSetupArgs, io: KtxCliIo, deps: KtxSetup
           {
             projectDir: projectResult.projectDir,
             inputMode: args.inputMode,
+            cliVersion: args.cliVersion,
+            runtimeInstallPolicy: setupRuntimeInstallPolicy(args),
             ...(args.embeddingBackend ? { embeddingBackend: args.embeddingBackend } : {}),
             ...(args.embeddingApiKeyEnv ? { embeddingApiKeyEnv: args.embeddingApiKeyEnv } : {}),
             ...(args.embeddingApiKeyFile ? { embeddingApiKeyFile: args.embeddingApiKeyFile } : {}),