Run mkdir before creating BuildManifest.apk

mkdir on the directory of a ninja output is usually not necessary, since
ninja creates the directory of all outputs of a build graph edge before
running the build graph cmd. However, the command of creating the
filesystem runs `rm -rf` on the intermediates filesystem directory,
undoing the mkdir created by ninja.

This is an issue for system_ext specifically. system does not run into
this issue because it includes a dep `fsverity-release-cert-der` which
installs a file  in /etc/security/fsverity.

Test: m out/soong/.intermediates/build/soong/fsgen/aosp_cf_x86_64_phone_generated_system_ext_image/android_common/aosp_cf_x86_64_phone_generated_system_ext_image.img
Bug: 383144733
Change-Id: Ia65346e0185b355ec3854427e5df7994160088d3