Upgrade base image from Debian Bullseye (oldstable) to Bookworm (stable)

[tsibley]

Avail ourselves of newer (though still not new ;) software, in particular the SQLite CLI.

Checklist

• Checks pass

[tsibley]

I expect this to fail in many ways, but let's see what happens!

[tsibley]

CI error was during build of vcftools for the aarch64 image. Relevant part looks like:

#35 3.637 checking for aarch64-linux-gnu-pkg-config... no
#35 3.637 checking for pkg-config... /usr/bin/pkg-config
#35 3.638 checking pkg-config is at least version 0.9.0... yes
#35 3.639 checking for zlib... no
#35 3.646 configure: error: Package requirements (zlib) were not met:
#35 3.646 
#35 3.646 Package 'zlib', required by 'virtual:world', not found
#35 3.646 
#35 3.646 Consider adjusting the PKG_CONFIG_PATH environment variable if you
#35 3.646 installed software in a non-standard prefix.
#35 3.646 
#35 3.646 Alternatively, you may set the environment variables ZLIB_CFLAGS
#35 3.646 and ZLIB_LIBS to avoid the need to call pkg-config.
#35 3.646 See the pkg-config man page for more details.

We install zlib1g-dev, which pulls in zlib1g, with xx-apt-get. Is the problem that the target platform's aarch64-linux-gnu-pkg-config isn't being found and so the build platform's pkg-config is used, but zlib isn't installed for the build platform?

[tsibley]

Is the problem that the target platform's aarch64-linux-gnu-pkg-config isn't being found and so the build platform's pkg-config is used, but zlib isn't installed for the build platform?

Replicated the error locally and then validated that installing pkg-config with xx-apt-get prior to the vcftools build worked.

[tsibley]

The next CI failure

> [linux/arm64 final  4/23] RUN if [[ "linux/arm64" == linux/arm64 ]]; then       apt-get update && apt-get install -y --no-install-recommends           libopenblas-base       ;     fi:
0.707 Hit:1 http://deb.debian.org/debian bookworm InRelease
0.709 Hit:2 http://deb.debian.org/debian bookworm-updates InRelease
0.709 Hit:3 http://deb.debian.org/debian-security bookworm-security InRelease
0.793 Hit:4 https://deb.nodesource.com/node_18.x nodistro InRelease

13.16 Reading state information...
13.19 E: Unable to locate package libopenblas-base

is because libopenblas-base was only a transitional package in Bullseye subsequently removed in Bookworm in favor of the new name, libopenblas0. We probably should have used libopenblas0 back then instead of the transitional package. Fixed in repush.

[tsibley]

The image built completely in CI but one minor testing failure because I'd based this branch on a month-old master (only visible on the workflow push event, not the workflow pull_request event). Whoops. Rebased to fix, but this is ready for review.

[victorlin]

I didn't test anything but changes look good.

[tsibley]

The ncov-ingest image seems to build fine locally if I rebase it onto this PR's image.