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/ui/app-boot/tests/profile.spec.ts

@@ -56,14 +56,14 @@ describe('resolveProfileDir', () => {
 })
 
 describe('initProfile', () => {
-  it('creates manifest, user patch layer, and npmrc once, never overwriting', () => {
+  it('creates manifest, user patch layer, and pnpm workspace once, never overwriting', () => {
     const home = tmp()
     const dir = resolveProfileDir('tui', home)
     initProfile(dir, ['@deepseek-ai/dsh-base'])
     const manifest = readProfileManifest('t', dir)
     expect(manifest.dsh?.plugins).toEqual(['@deepseek-ai/dsh-base'])
     expect(readFileSync(join(dir, PROFILE_PATCH_FILENAME), 'utf8')).toContain('[]')
-    expect(readFileSync(join(dir, '.npmrc'), 'utf8')).toContain('node-linker=hoisted')
+    expect(readFileSync(join(dir, 'pnpm-workspace.yaml'), 'utf8')).toContain('nodeLinker: hoisted')
     // Re-init keeps user edits.
     writeFileSync(join(dir, PROFILE_PATCH_FILENAME), '- id: x\n  config: {}\n')
     initProfile(dir, ['other'])