[PWA] Shutdown commands during profile manager deletion

Previously, the WebAppCommandManager would shutdown itself and clean up
all dependencies (like the WebContents it owns) as part of profile
deletion. This missed the use-case where certain KeyedServices that the
WebContents relied on would be destroyed BEFORE the destruction of the
WebContents, leading to crashes happening sporadically.

This CL attempts to fix that by shutting down the command manager also
during profile manager shutdown, so that the WebContents can be cleaned
up BEFORE the profile deletion triggers a shutdown of the command
manager. This serves as a speculative fix for crbug.com/415776884.

Bug: 415776884
Change-Id: I99dc5ffd85101bbf0efa8343a598a5e527cc6afd
Reviewed-on: https://chromium-review.googlesource.com/c/chromium/src/+/6514228
Commit-Queue: Dibyajyoti Pal <dibyapal@chromium.org>
Reviewed-by: May Siem <msiem@chromium.org>
Reviewed-by: Daniel Murphy <dmurph@chromium.org>
Cr-Commit-Position: refs/heads/main@{#1455896}