Build only the modules JASP ships, not the developer helper's 22

Modules/modules-settings.json splits modules into 'common' - the seven
bundled with the application - and 'extra', which JASP fetches on demand
into ~/.local/share/JASP. buildAllDefaultJaspModules.R builds 22 regardless:
it is a developer convenience for having everything locally, not a
definition of what a release contains. I had been treating it as the latter.

The cost of that mistake was not just size. Most of the blockers this build
hit came from modules that are never shipped: gsl blocked jaspNetwork and
jaspBFF, OpenMx blocked jaspSem - all 'extra'. Building the right list drops
them entirely.

Measured: the seven common modules come to ~2.3 GB against ~8.3 GB for all
22. Bundles are already zstd-compressed, so the tarball does not shrink them
further; ~2.5-3 GB total is the realistic figure, against the Flatpak's
1.4 GB. The remaining gap is bundleAll=TRUE giving every module its own copy
of its R dependencies.

The guard now names the modules it expects and reports which are missing.

build/build-jasp.sh

@@ -52,7 +52,8 @@ pacman -Syu --noconfirm --needed \
   boost boost-libs glpk jsoncpp libarchive openssl curl sqlite zlib \
   readstat netcdf mpfr cairo pango fontconfig harfbuzz fribidi icu pcre2 \
   readline bzip2 xz libpng libtiff libjpeg-turbo minizip \
-  libxkbcommon libxkbcommon-x11 libxt wget unzip python
+  libxkbcommon libxkbcommon-x11 libxt wget unzip python \
+  gsl libsodium gmp nlopt libxml2 fftw
 
 # Stock makepkg.conf leaves MAKEFLAGS at -j1, which makes the AUR dependencies
 # (JAGS especially) crawl.
@@ -269,12 +270,46 @@ R_JOBS="${R_JOBS:-2}"
 export MAKEFLAGS="-j${R_JOBS}"
 log "compiling R packages with -j${R_JOBS} (OpenMx needs the headroom)"
 
-EXPECTED_MODULES=22
+# Build only the modules JASP actually ships. Modules/modules-settings.json
+# splits them into "common" (bundled with the application) and "extra"
+# (fetched on demand at runtime, into ~/.local/share/JASP).
+#
+# buildAllDefaultJaspModules.R is a *developer* helper that builds 22 modules
+# regardless of that split — its name says "all default modules", not "what is
+# released". Building from it produces a ~9 GB tree, most of it modules the user
+# would have downloaded on demand anyway, and drags in system dependencies that
+# only the extras need (gsl for jaspNetwork, OpenMx for jaspSem).
+mapfile -t COMMON_MODULES < <(
+  python3 -c "
+import json
+print('\n'.join(json.load(open('../Modules/modules-settings.json'))['common']))
+"
+)
+log "shipping the ${#COMMON_MODULES[@]} common modules: ${COMMON_MODULES[*]}"
+
+mkdir -p ModuleBundleBuildDir/Modules
+for module in "${COMMON_MODULES[@]}"; do
+  if [[ ! -d "ModuleBundleBuildDir/Modules/${module}" ]]; then
+    log "cloning ${module}"
+    git clone --depth 1 "https://github.com/jasp-stats/${module}" \
+      "ModuleBundleBuildDir/Modules/${module}"
+  fi
+done
+
+EXPECTED_MODULES="${#COMMON_MODULES[@]}"
+MODULE_PATHS=()
+for module in "${COMMON_MODULES[@]}"; do
+  MODULE_PATHS+=("ModuleBundleBuildDir/Modules/${module}")
+done
+
 for attempt in 1 2 3; do
   log "module build pass ${attempt}/3"
-  Rscript buildAllDefaultJaspModules.R || true
-  built="$(find "$MODULE_BUNDLES" -mindepth 1 -maxdepth 1 2>/dev/null | wc -l)"
-  log "pass ${attempt} finished: ${built}/${EXPECTED_MODULES} bundles"
+  ./buildModuleBundlesLocally.R "${MODULE_PATHS[@]}" || true
+  built=0
+  for module in "${COMMON_MODULES[@]}"; do
+    [[ -f "${MODULE_BUNDLES}/${module}.JASPModule" ]] && built=$((built + 1))
+  done
+  log "pass ${attempt} finished: ${built}/${EXPECTED_MODULES} common modules"
   [[ "$built" -ge "$EXPECTED_MODULES" ]] && break
 done
 
@@ -287,15 +322,17 @@ fi
 
 # Guard on the expected count, not merely "non-empty". An earlier run shipped a
 # package containing 2 of 22 modules because a non-empty check passed.
-bundle_count="$(find "$MODULE_BUNDLES" -mindepth 1 -maxdepth 1 2>/dev/null | wc -l)"
-if [[ "$bundle_count" -lt "$EXPECTED_MODULES" ]]; then
-  echo "error: only ${bundle_count}/${EXPECTED_MODULES} module bundles were built" >&2
-  echo "       system2() in buildAllDefaultJaspModules.R hides the real error;" >&2
+missing=()
+for module in "${COMMON_MODULES[@]}"; do
+  [[ -f "${MODULE_BUNDLES}/${module}.JASPModule" ]] || missing+=("$module")
+done
+if [[ ${#missing[@]} -gt 0 ]]; then
+  echo "error: ${#missing[@]} of ${EXPECTED_MODULES} common modules were not built" >&2
+  printf '       missing: %s\n' "${missing[@]}" >&2
   echo "       search the log above for 'failed to install'" >&2
-  find "$MODULE_BUNDLES" -mindepth 1 -maxdepth 1 -printf '       have: %f\n' 2>/dev/null >&2
   exit 1
 fi
-log "module build produced ${bundle_count} bundles"
+log "all ${EXPECTED_MODULES} common modules built"
 
 # -------------------------------------------------------------------- staging
 log "staging install tree"
@@ -356,7 +393,7 @@ staged_r="$STAGE_DIR$PREFIX/R/lib/R/lib"
 for lib in libR.so libRblas.so libRlapack.so; do
   [[ -f "$staged_r/$lib" ]] || { echo "error: staged tree lacks $lib" >&2; exit 1; }
 done
-staged_bundles="$(find "$STAGE_DIR$PREFIX/Modules" -mindepth 1 -maxdepth 1 2>/dev/null | wc -l)"
+staged_bundles="$(find "$STAGE_DIR$PREFIX/Modules" -maxdepth 1 -name '*.JASPModule' 2>/dev/null | wc -l)"
 [[ "$staged_bundles" -gt 0 ]] || { echo "error: staged tree has no module bundles" >&2; exit 1; }
 staged_so="$(find "$STAGE_DIR$PREFIX" -name '*.so' 2>/dev/null | wc -l)"
 log "staged: ${staged_bundles} module bundles, ${staged_so} shared objects"