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/dump-config.ts

@@ -29,7 +29,10 @@ const NAME = 'dsh'
  */
 export function runDumpConfig(profile: string, defaultOnly: boolean, patches: readonly string[]): void {
   healProfilesModuleFallback(INSTALL_ANCHOR)
-  const loaded = loadProfile(NAME, profile, INSTALL_ANCHOR)
+  // The default dump never reads the user layer: it doubles as the recovery
+  // diagnostic for a broken cordis.patch.yml, so parsing that file here would
+  // defeat its purpose.
+  const loaded = loadProfile(NAME, profile, INSTALL_ANCHOR, undefined, { userLayer: !defaultOnly })
   const layers: ConfigDumpLayer[] = loaded.layers.map(layer => ({
     label: layer.packageName,
     patches: layer.patches,