Keep the bundled R on the rpath, and stop makepkg tidying the tree

First run of the actual binary: ldd reported 'libR.so => not found'.

patchelf --set-rpath replaces the existing rpath rather than appending, so
setting it to $PREFIX/lib discarded the -Wl,-rpath the build had given the
JASP binary for the bundled R. Every other bundled library resolved; only R
went missing, because libR.so/libRblas.so/libRlapack.so live under
R/lib/R/lib rather than in the bundled lib directory. The rpath now lists
both.

Two smaller things the same run surfaced:

- makepkg ran its tidying steps on a tree that was already built and
  verified - removing libtool and static library files, purging, compressing
  man pages. For a -bin package that is a difference between what was tested
  and what gets installed. All of them are now disabled.
- /opt/jasp-desktop/bin/JASP was not on PATH; the package now symlinks
  /usr/bin/jasp.

build/bundle-libs.sh

@@ -95,11 +95,18 @@ chmod u+w "$LIBDIR"/*.so* 2>/dev/null || true
 # An absolute rpath is safe here because the tarball always unpacks to $PREFIX;
 # it avoids $ORIGIN arithmetic across bin/, R/lib/R/lib/ and the per-package
 # libs/ directories, which all sit at different depths.
-echo ":: setting rpath on ELF objects"
+#
+# Both directories must be listed. patchelf --set-rpath *replaces* the existing
+# rpath rather than appending to it, so setting only $PREFIX/lib discards the
+# -Wl,-rpath the build gave the JASP binary for the bundled R and leaves
+# "libR.so => not found". libR.so, libRblas.so and libRlapack.so live under
+# R/lib/R/lib, not in the bundled lib directory.
+RPATH="${PREFIX}/lib:${PREFIX}/R/lib/R/lib"
+echo ":: setting rpath to ${RPATH}"
 patched=0
 for obj in "${elf_files[@]}" "$LIBDIR"/*.so*; do
   [[ -f "$obj" ]] || continue
-  if patchelf --set-rpath "${PREFIX}/lib" "$obj" 2>/dev/null; then
+  if patchelf --set-rpath "$RPATH" "$obj" 2>/dev/null; then
     patched=$((patched + 1))
   fi
 done

packaging/PKGBUILD.in

@@ -44,10 +44,12 @@ depends=(
   'fontconfig' 'freetype2' 'libxkbcommon' 'hicolor-icon-theme'
 )
 
-# The tarball is a complete /opt + /usr install tree. Stripping would be slow and
-# is a good way to break a bundled R plus several hundred compiled R modules;
-# the rpath set at build time must also survive untouched.
-options=('!strip' '!debug')
+# The tarball is a complete, already-verified /opt + /usr install tree, so every
+# one of makepkg's tidying steps is unwanted here: they would modify content
+# that was tested in exactly this form. Stripping in particular would be slow
+# and is a good way to break a bundled R plus several hundred compiled R
+# modules, and the rpath set at build time must survive untouched.
+options=('!strip' '!debug' '!libtool' '!staticlibs' '!zipman' '!purge' '!emptydirs')
 
 source=("jasp-desktop-${pkgver}-${pkgrel}-x86_64.tar.zst::@DOWNLOAD_URL@")
 sha256sums=('@SHA256@')
@@ -55,4 +57,8 @@ sha256sums=('@SHA256@')
 package() {
   cp -a "${srcdir}/opt" "${pkgdir}/opt"
   cp -a "${srcdir}/usr" "${pkgdir}/usr"
+
+  # The application lives under /opt; give it a name on PATH.
+  install -d "${pkgdir}/usr/bin"
+  ln -s /opt/jasp-desktop/bin/JASP "${pkgdir}/usr/bin/jasp"
 }