Add the SQLite CLI for augur merge

[tsibley]

Ideally this would have been added before or as Augur 25.3.0—the first version to include augur merge—was packaged into this runtime, but I plain forgot.

Checklist

• Checks pass

[tsibley]

Oh, ugh. Our images are based on Debian Bullseye (currently "oldstable"), which packages SQLite 3.34, but augur merge requires ≥3.39. Phooey.

I can either

1. Upgrade image base to Debian Bookworm (currently "stable"), which packages 3.40. We'll eventually want to do this anyway, but it's a much more wide reaching change and potentially not trivial.
2. Install an appropriate SQLite version from elsewhere, either binaries or compiled from source.

[tsibley]

Throwing #233 (option 1) at the wall to see what sticks.

[tsibley]

Option 2 probably looks something like this:

diff --git a/Dockerfile b/Dockerfile
index e804b8c..0af2117 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -109,6 +109,17 @@ RUN curl -fsSL https://api.github.com/repos/vcftools/vcftools/tarball/1cab5204eb
  && cp -rp built/bin/*    /final/bin \
  && cp -rp built/share/*  /final/share
 
+# Build SQLite CLI
+WORKDIR /build/sqlite
+RUN curl -fsSL --proto 'https=' https://sqlite.org/2024/sqlite-autoconf-3460100.tar.gz \
+  | tar xzvpf - --no-same-owner --strip-components=1 \
+ && CFLAGS="-Os" ./configure --prefix=$PWD/built \
+      --build=$(TARGETPLATFORM= xx-clang --print-target-triple) \
+      --host=$(xx-clang --print-target-triple) \
+ && make && make install \
+ && cp -rp built/bin/*    /final/bin \
+ && cp -rp built/share/*  /final/share
+
 
 # 2. Download pre-built programs
 

[tsibley]

Option 1 in #233 is going to work, it seems, without too much additional effort (and it's effort we'd want/need to do eventually anyway).