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.

apps/cli/src/plugin.ts

@@ -57,7 +57,10 @@ function reconcilePlugins(before: ProfileManifest, profileDir: string): void {
   for (const packageName of afterDeps) {
     if (beforeDeps.has(packageName) || plugins.includes(packageName)) continue
     if (!exportsPatch(packageName, profileDir)) {
-      process.stderr.write(`${NAME}: warning: ${packageName} declares no dsh.patch — installed as a plain dependency, not a profile layer\n`)
+      process.stderr.write(
+        `${NAME}: warning: ${packageName} declares no dsh.patch — installed as a plain dependency, not a profile layer `
+        + '(if it gains one later, add it to dsh.plugins in the profile\'s package.json)\n',
+      )
       continue
     }
     plugins.push(packageName)