fix(setup): write app-behavior flags to every env file the app can start from

The wizard wrote the Chat opt-out only to the env file its own mode owns, so
choosing compose put it in the root `.env` while `bun run dev` reads
`apps/sim/.env` and never saw it. Skipping the chat key appeared to do nothing.

Mirror values that change how the app behaves — as opposed to where it connects
— across both targets. Connection settings deliberately do not go through this:
DATABASE_URL and friends differ between the compose stack and a local dev run,
which is why this takes an explicit set of values rather than the whole batch.

The mirrored file is written even when absent, since missing is exactly the case
that stranded the flag, but with seeding suppressed so a compose run leaves a
one-line apps/sim/.env instead of a full .env.example for a stack the user is
not running.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012ErcRgvi7VQBeKDQ3MBMha

Author: TheodoreSpeaks

package.json

@@ -65,7 +65,7 @@
     "skills:sync": "bun run scripts/sync-skills.ts",
     "skills:check": "bun run scripts/sync-skills.ts --check",
     "setup": "bun install && bun run scripts/setup/index.ts setup",
-    "sim": "bun run scripts/setup/index.ts",
+    "sim": "bun install && bun run scripts/setup/index.ts",
     "doctor": "bun run scripts/setup/index.ts doctor",
     "agent-stream-docs:generate": "bun run scripts/sync-agent-stream-docs.ts",
     "agent-stream-docs:check": "bun run scripts/sync-agent-stream-docs.ts --check",

scripts/setup/env-files.ts

@@ -105,14 +105,25 @@ export function upsertEnv(content: string, key: string, value: string): string {
   return lines.join('\n')
 }
 
-/** Writes values into an env file, seeding a missing file from its .env.example. */
-export function writeEnvValues(target: EnvTarget, values: Record<string, string>): void {
+/**
+ * Writes values into an env file, seeding a missing file from its `.env.example`.
+ *
+ * `seedFromExample: false` creates a missing file holding only `values` instead.
+ * Used when mirroring one flag into a target the user did not choose, where
+ * materializing a whole example for a stack they are not running would be
+ * surprising.
+ */
+export function writeEnvValues(
+  target: EnvTarget,
+  values: Record<string, string>,
+  { seedFromExample = true }: { seedFromExample?: boolean } = {}
+): void {
   const filePath = ENV_PATHS[target]
   let content: string
   if (existsSync(filePath)) {
     content = readFileSync(filePath, 'utf8')
   } else {
-    const example = EXAMPLE_PATHS[target]
+    const example = seedFromExample ? EXAMPLE_PATHS[target] : undefined
     content = example && existsSync(example) ? readFileSync(example, 'utf8') : ''
   }
   for (const [key, value] of Object.entries(values)) {

scripts/setup/modes/compose.ts

@@ -17,6 +17,7 @@ import {
   promptSignInProviders,
   promptStorage,
   promptUnlocks,
+  writeAppBehaviorValues,
 } from '../steps.ts'
 import { glyph, theme } from '../theme.ts'
 
@@ -113,7 +114,7 @@ export async function runComposeMode(detection: Detection, quick: boolean): Prom
   Object.assign(values, mothershipOverride())
   const copilotKey = await promptCopilotKey(root.vars.get('COPILOT_API_KEY'))
   if (copilotKey) values.COPILOT_API_KEY = copilotKey
-  Object.assign(values, chatFlagValues(copilotKey))
+  writeAppBehaviorValues('root', chatFlagValues(copilotKey))
   Object.assign(values, await promptLlmKeys(detection, !quick))
   if (!quick) {
     const storage = await promptStorage(root.vars, true)

scripts/setup/modes/dev.ts

@@ -19,6 +19,7 @@ import {
   promptSignInProviders,
   promptStorage,
   promptUnlocks,
+  writeAppBehaviorValues,
 } from '../steps.ts'
 import { glyph, theme } from '../theme.ts'
 
@@ -125,7 +126,7 @@ export async function runDevMode(
   Object.assign(values, mothershipOverride())
   const copilotKey = await promptCopilotKey(simAfter.vars.get('COPILOT_API_KEY'))
   if (copilotKey) values.COPILOT_API_KEY = copilotKey
-  Object.assign(values, chatFlagValues(copilotKey))
+  writeAppBehaviorValues('sim', chatFlagValues(copilotKey))
   Object.assign(values, await promptLlmKeys(detection, !quick))
 
   // Redis is set up in every mode, quick included. Storage falls back to

scripts/setup/steps.ts

@@ -2,12 +2,14 @@ import { browserKeyFlow } from './cli-auth.ts'
 import type { Detection } from './detect.ts'
 import {
   type EnvFile,
+  type EnvTarget,
   generateSecret,
   isPlaceholder,
   isTruthy,
   isUsableSecret,
   SECRET_KEYS,
   secretRequirement,
+  writeEnvValues,
 } from './env-files.ts'
 import * as p from './prompter.ts'
 import { link, theme } from './theme.ts'
@@ -80,6 +82,32 @@ export function chatFlagValues(copilotKey: string | null): Record<string, string
   return { NEXT_PUBLIC_CHAT_DISABLED: copilotKey ? 'false' : 'true' }
 }
 
+/**
+ * Env files the app reads its own configuration from: `apps/sim/.env` when
+ * started with `bun run dev`, the root `.env` when started through
+ * docker-compose.
+ */
+const APP_ENV_TARGETS = ['sim', 'root'] as const satisfies readonly EnvTarget[]
+
+/**
+ * Writes values that change how the app behaves — as opposed to where it
+ * connects — to every env file the app might be started from, so the outcome
+ * follows what the user answered rather than which command they later use to
+ * launch Sim. Connection settings must NOT go through this: `DATABASE_URL` and
+ * friends legitimately differ between the compose stack and a local dev run.
+ *
+ * Mirrored targets are written even when absent, because the file being missing
+ * is precisely the case that strands the flag — but without seeding from
+ * `.env.example`, so a compose run leaves behind a one-line `apps/sim/.env`
+ * rather than a full example for a stack the user is not running.
+ */
+export function writeAppBehaviorValues(primary: EnvTarget, values: Record<string, string>): void {
+  writeEnvValues(primary, values)
+  for (const target of APP_ENV_TARGETS) {
+    if (target !== primary) writeEnvValues(target, values, { seedFromExample: false })
+  }
+}
+
 /**
  * Escape hatch for Sim devs pointing an install at a non-prod mothership:
  *