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/args.ts

@@ -168,9 +168,19 @@ Examples:
         if (defaultOnly && patches.length > 0) {
           program.error('error: --dump-default-config prints the bundle layers and takes no --patch')
         }
+        // The dump is boot-free and does not derive flag patches; silently
+        // dropping them would print a tree that differs from the same
+        // invocation's boot.
+        if (options.host !== undefined || options.port !== undefined || options.dev === true
+          || options.workspaceRoot !== undefined || options.trustedHost !== undefined) {
+          program.error('error: config dumps take no web flags (--host/--port/--dev/--workspace-root/--trusted-host)')
+        }
         resolved = { mode: 'dump-config', profile: 'web', defaultOnly, patches }
         return
       }
+      if (options.port !== undefined && !/^\d+$/.test(options.port)) {
+        program.error(`error: --port must be a number, got ${JSON.stringify(options.port)}`)
+      }
       resolved = {
         mode: 'web',
         patches,