fix(review): audit prepared-wrapper activation and pin generated shapes

ds-review-bot round 1 on the DSH-home integration:
- generated wrappers now inject the services their manifest needs (skills/
  tools beside loader), and loadPreparedRepository rejects a wrapper fiber
  that settles anything but ACTIVE — a composition missing a required
  service fails the repository transaction instead of committing an ACTIVE
  row over a silently PENDING child (critical finding)
- the github: source ref segment excludes '#', so 'a#b' refs fail at the
  config parser with the promised syntax instead of inside pnpm
- watchPersonalPatches re-reads the include's non-patch options per refresh
  instead of a registration-time snapshot
- the TUI smoke's cache-seeded wrapper is produced by the real
  prepareDshPlugin (cache LAYOUT stays a deliberate external pin)
- new Loader integration test drives a live repositories update through
  entry.update: generation swap, old skills removed, failed candidate
  rolled back to the previous generation

packages/ui/app-boot/src/index.ts

@@ -323,8 +323,11 @@ export async function watchPersonalPatches(
   const entry = bootstrapIncludes.get(ctx)
   if (entry === undefined) throw new Error(`${binName}: personal config watching requires the root Include entry`)
   const filename = join(dir, PERSONAL_CONFIG_FILENAME)
-  const { patches: _initialPatches, ...includeConfig } = entry.options.config as Include.Config
   return hmr.registerConfig(filename, async () => {
+    // Re-read the include's non-patch options per refresh: a writer that
+    // updates the root Include's other options between refreshes (none exists
+    // today) must not have them silently reverted by a personal reload.
+    const { patches: _previousPatches, ...includeConfig } = entry.options.config as Include.Config
     const personalPatches = loadPersonalPatches(binName, dir) ?? []
     const patches = compose(personalPatches)
     await entry.update({