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.

pnpm-lock.yaml

@@ -161,6 +161,15 @@ importers:
       '@deepseek-ai/dsh-pty-local':
         specifier: workspace:^
         version: link:../../packages/pty/pty-local
+      '@deepseek-ai/dsh-session-reference':
+        specifier: workspace:^
+        version: link:../../packages/context/session-reference
+      '@deepseek-ai/dsh-tmux-context':
+        specifier: workspace:^
+        version: link:../../packages/context/tmux-context
+      '@deepseek-ai/dsh-tool-ask-user':
+        specifier: workspace:^
+        version: link:../../packages/ui/tool-ask-user
       '@deepseek-ai/dsh-tool-bash-persistent':
         specifier: workspace:^
         version: link:../../packages/pty/tool-bash-persistent
@@ -1053,6 +1062,9 @@ importers:
         specifier: ^3.18.0
         version: link:../../../vendor/schemastery
     devDependencies:
+      '@cordisjs/plugin-loader':
+        specifier: workspace:^
+        version: link:../../../vendor/loader
       '@deepseek-ai/dsh-agent':
         specifier: workspace:^
         version: link:../../core/agent