fix: repair build cache preflight and hide companion bubbles on focus

[GCWing]

Summary

Repairs two build-cache defects and one Agent companion interaction issue:

• check:build-prereqs now detects a pnpm virtual store package whose directory
  exists but holds no files (or whose link target is gone). The matching
  node_modules/.bin shim then resolves to a path without content, and nested
  tools fail with a confusing Cannot find module .../bin/<tool> error.
  pnpm install does not repair that state, so --fix removes the broken
  directories first, guarded so a repair can never delete anything outside the
  virtual store.
• The mobile-web rebuild cache watched a hand-written list of design-system
  sources, so a change under design-system/packages/ui or a package-root file
  such as vite.config.ts could leave src/mobile-web/dist stale while the
  build still reported success. It now watches the design-system/packages/
  and design-system/tooling/ trees (generated dist/ and node_modules/
  stay ignored), and the contract test runs in CI.
• The Agent companion pet hides its bubbles while the main window is focused.
  The main window forwards focus changes as
  agent-companion://main-window-state; the pet keeps its bubble list empty
  while that flag is set and resizes back to the pet alone, so the overlay no
  longer covers the session the user is working in.

Type and Areas

Type: bug fix (build tooling/CI), behavior fix (web UI Agent companion)

Areas: build scripts + CI, Web UI (Agent companion desktop pet)

Motivation / Impact

Both build-cache defects cost real debugging time:

• A package directory that pnpm records but leaves empty makes every nested
  tool invocation fail with an error that points at the bin shim rather than at
  the real cause.
• A stale src/mobile-web/dist silently serves an old mobile bundle, and small
  viewport work was the first thing to notice.

No direct user-facing change for the first two. The Agent companion change is
user-visible on Desktop: bubbles stay out of the way while the main window has
focus and reappear when it loses focus.

Verification

• node --test scripts/mobile-web-build.test.mjs -> 7 passed
• node --test scripts/check-build-prereqs.test.mjs -> 10 passed
• pnpm run lint:web -> 0 errors (9 pre-existing warnings)
• pnpm run type-check:web -> passed
• pnpm --dir src/web-ui exec vitest run src/app/components/AgentCompanionDesktopPet -> 21 passed
• pnpm run check:github-config -> GitHub YAML audit passed for 15 files

Not run: any GUI/visual check of the pet window on Desktop; the companion change
is covered by the component tests and the window-focus wiring only.

Note for reviewers: scripts/check-github-config.test.mjs reports 3 failures on
a clean origin/main checkout in this environment (release/beta workflow
assertions unrelated to this PR); the audit script that CI runs passes.

Reviewer Notes

The two build-cache fixes and the companion change are independent; they are
bundled because they came from the same working tree. Files do not overlap, so
either part can be dropped without touching the other.

Checklist

• This PR does not include secrets, temporary prompts, generated scratch files, or unrelated artifacts.
• Relevant verification is recorded above, or skipped checks are explained.
• User-facing strings, docs, and locales are updated where applicable. (No user-visible strings added; companion copy is unchanged.)