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/web/tests/scaffold.ts

@@ -1,7 +1,8 @@
 // Shared scaffold for the keyless browser e2e lane (Agent Note:
 // .agents/notes/implemented/testing/2026-07-24-web-gui-browser-e2e-lane.md).
-// Boots the REAL web composition — the shipped base plus web overlay through
-// the vendored Loader (the same include boot AppCLIEntry drives), patched the
+// Boots the REAL web composition — the dsh-base and dsh-web-app bundle
+// patches over the empty profile root through the vendored Loader (the same
+// layer stack the profile boot composes), patched the
 // snapshot way — so a real chromium exercises the real HTTP uplink/WebSocket
 // downlink, api-gateway, agent loop, tools, and persistence. Modes ride $DSH_SNAPSHOT:
 // replay (default, keyless: normally disables the llm-deepseek row and