504f030995a07120830b60b40619840c21fe72f9
markd
  Fri Jul 24 10:58:20 2026 -0700
submoduleSetup: sync submodules to pinned commit on every build

Run 'git submodule update --init --recursive' unconditionally when in a git
work tree, rather than only when the submodule was uninitialized.  This means
a moved submodule pointer (e.g. after a pull) is checked out on every build,
and --recursive keeps the nested htscodecs submodule in sync too.  git is
silent when already in sync.  The non-git-work-tree (source release) branch
is unchanged.

No RM.

diff --git src/submodules/submoduleSetup src/submodules/submoduleSetup
index 4834fda73d7..353802f8111 100755
--- src/submodules/submoduleSetup
+++ src/submodules/submoduleSetup
@@ -1,41 +1,42 @@
 #!/bin/bash
 set -beEu -o pipefail
 
 # Do required submodule setup to support building the browser
-# If need, do the submodule init, also check from having remains of
-# old htslib copy to deal with switch from old version.
+# Sync submodules to the commits pinned by the parent repo, and check for
+# having remains of old htslib copy to deal with switch from old version.
 
 if [ -e htslib ] ; then
     echo "*********************************************************************" >&2
     echo "Note: an outdated kent/src/htslib/ exists in the working tree." >&2
     echo "      It is no longer used and can be removed."   >&2
     echo "*********************************************************************" >&2
 fi
 
-if [ !  -e submodules/htslib/.git -o ! -e submodules/htslib/htscodecs/.git ] ; then
 if git rev-parse --is-inside-work-tree >/dev/null 2>&1 ; then
-        echo "Note: initializing git submodules" >&2
-        (set -x; git -c protocol.file.allow=always submodule update --init --recursive)
+    # Sync submodules to the commits pinned by the parent repo on every build,
+    # not just on first-time init, so a moved pointer (e.g. after a pull) is
+    # always checked out.  --init covers the first-time case, --recursive also
+    # updates the nested htscodecs submodule.  git is silent when already in sync.
+    git -c protocol.file.allow=always submodule update --init --recursive
 elif [ ! -e submodules/htslib/hts.c -o ! -e submodules/htslib/htscodecs/htscodecs/htscodecs.c ] ; then
     # not a git working tree (e.g. a source release); submodule sources must
     # already be present since they can not be checked out without git.
     echo "Error: submodule sources under submodules/htslib are missing and this" >&2
     echo "       is not a git working tree, so they can not be initialized." >&2
     exit 1
 fi
-fi
 
 # Generate htslib's compiler-probe makefile fragment (htscodecs.mk) and config.h
 # SERIALLY, here, before the parallel ("make -j") build descends into htslib.
 # hts_probe_cc.sh probes SIMD (SSE4/AVX2/AVX512) support using fixed-name
 # conftest.* temp files in submodules/htslib/.  Under -j, a concurrent writer
 # can clobber conftest.c between its creation and compilation, so the AVX2 probe
 # "succeeds" with no -mavx2 flag; that records HTS_BUILD_AVX2=1 with an empty
 # HTS_CFLAGS_AVX2 in htscodecs.mk.  config.h then defines HAVE_AVX2, enabling
 # AVX2 source that is compiled without -mavx2 -> "target specific option
 # mismatch" build failure.  Both files are no-prerequisite make targets, so the
 # corrupt result is cached and reused until deleted.  Building them single-
 # threaded here guarantees the probe runs exactly once and the -j build never
 # triggers it.  Only done when they are missing, so it does not force needless
 # htslib recompiles on incremental builds.
 if [ -e submodules/htslib/Makefile ] && \