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/headless/cordis.patch.yml

@@ -1,6 +1,7 @@
 # The dsh-headless bundle patch: one-shot task mode over dsh-base +
 # dsh-web-app. The web composition stays mounted (the session is observable
-# in a browser while it runs); this layer silences the URL line, moves the
+# in a browser while it runs); this layer silences the URL line and the
+# GUI-orientation surface context (this user is not in the GUI), moves the
 # webserver to an OS-assigned port so parallel headless runs never collide,
 # and mounts the one-shot runner. The launcher patches the runner's `task`.
 
@@ -13,6 +14,7 @@
   config:
     mode: production
     printUrl: false
+    surfaceContext: false
 
 - insert:
     - id: headless-runner