fix: address ds-review-bot round — insert-aliasing clones, settlement gates, closure module fallback

- Clone patch lists per generation (boot + composeLive): the include pushes
  insert rows by reference and mutates them in place, so a reused object
  baked user overrides into bundle rows and removal could not revert; the
  built-bin hot-reload e2e now asserts an override AND its removal reverting.
- The headless runner awaits Loader settlement before prompting (its inject
  gate covers only apiProxy/httpServer) and abandons cleanly when the tree
  died during the wait.
- healProfilesModuleFallback walks the app's full dependency+peer closure:
  out-of-tree plugins import seam packages (dsh-compact, dsh-subprocess, ...)
  that only implementations reach, and peers are how seams are declared.
- Profile init writes pnpm-workspace.yaml (nodeLinker: hoisted), not .npmrc
  — pnpm >=10 reads settings from the workspace manifest.
- Web dumps reject boot-only flags instead of printing a tree that differs
  from the same invocation's boot; --port validates at the flag;
  --dump-default-config no longer parses the (possibly broken) user layer;
  trustedHosts flag derivation merges over the composed value instead of
  replacing it; web-runtime gains surfaceContext (headless disables the GUI
  prompt/bash-vars the old -p never mounted); 'node_modules' is a reserved
  profile name; plugin-warning names the recovery step; client AGENTS.md
  registration surfaces point at the web-app bundle.
- Ship session-reference/tmux-context/tool-ask-user as app dependencies for
  terminal front-door patch layers (turtle-ui), same stance as mcp-client.

packages/bundle/web-app/src/index.ts

@@ -34,6 +34,13 @@ export interface Config {
   mode: WebMode
   /** Print the URL line on activation; a headless layer over this bundle turns it off. */
   printUrl: boolean
+  /**
+   * Register the model-visible surface context (the `app:web-surface` prompt
+   * section and the `DSH_WEB_URL`/`DSH_WEB_MODE` bash variables). A one-shot
+   * layer turns it off: its user is not interacting through the GUI, so the
+   * orientation text would be false.
+   */
+  surfaceContext: boolean
   /**
    * LAN IPv4 addresses sampled once by the launcher when the effective bind
    * is all-interfaces — the exact snapshot the /api trust fence was
@@ -46,6 +53,7 @@ export interface Config {
 export const Config: z<Config> = z.object({
   mode: z.union([z.const('production'), z.const('development')]).default('production'),
   printUrl: z.boolean().default(true),
+  surfaceContext: z.boolean().default(true),
   lanAddresses: z.array(String).default([]),
 })
 
@@ -104,23 +112,25 @@ export const internals: { resolveDistIndex: () => string } = { resolveDistIndex
  */
 export function apply(ctx: Context, config: Config): void {
   ctx.plugin(FrontendStatic, { distIndex: internals.resolveDistIndex() })
-  ctx.inject(['systemPrompt'], (promptCtx) => {
-    promptCtx.systemPrompt.section({
-      name: 'app:web-surface',
-      order: -98,
-      text: () => webSurfacePrompt(localWebUrl(promptCtx), config.mode),
+  if (config.surfaceContext) {
+    ctx.inject(['systemPrompt'], (promptCtx) => {
+      promptCtx.systemPrompt.section({
+        name: 'app:web-surface',
+        order: -98,
+        text: () => webSurfacePrompt(localWebUrl(promptCtx), config.mode),
+      })
     })
-  })
-  ctx.inject(['bashEnv'], (runtimeCtx) => {
-    runtimeCtx.bashEnv.register({
-      name: 'web-runtime',
-      variables: {
-        [DSH_WEB_URL]: { description: 'Canonical local URL of the DeepSeek Harness Web GUI serving this session.' },
-        [DSH_WEB_MODE]: { description: 'Web runtime mode: production, or development when the client-plugin HMR receiver is active.' },
-      },
-      resolve: () => ({ [DSH_WEB_URL]: localWebUrl(runtimeCtx), [DSH_WEB_MODE]: config.mode }),
+    ctx.inject(['bashEnv'], (runtimeCtx) => {
+      runtimeCtx.bashEnv.register({
+        name: 'web-runtime',
+        variables: {
+          [DSH_WEB_URL]: { description: 'Canonical local URL of the DeepSeek Harness Web GUI serving this session.' },
+          [DSH_WEB_MODE]: { description: 'Web runtime mode: production, or development when the client-plugin HMR receiver is active.' },
+        },
+        resolve: () => ({ [DSH_WEB_URL]: localWebUrl(runtimeCtx), [DSH_WEB_MODE]: config.mode }),
+      })
     })
-  })
+  }
   if (config.printUrl) {
     // The URL line is a readiness signal: supervisors (and the keyless CLI
     // smoke) RPC as soon as they observe it, so it must not print while