diff --git a/.cargo/config.toml b/.cargo/config.toml
index 9037819ed..96522a110 100644
--- a/.cargo/config.toml
+++ b/.cargo/config.toml
@@ -4,11 +4,9 @@ rustflags = ["-C", "link-args=-rdynamic"]
 [target.x86_64-unknown-linux-gnu]
 rustflags = ["-C", "link-args=-rdynamic"]
 
-# Since autotools sets this and we are *not* forcing it here, this will not
+# Since autotools sets these and we are *not* forcing them here, this will not
 # affect release builds. It will affect `cargo run` and make it easier to test
 # locally since the Lua loader path will be relative to the current sources.
-# For debug builds it is assumed you configured `--without-system-luarocks`,
-# this convenience won't enable you to use system packages in debug builds.
 [env]
 SILE_PATH = { value = "", relative = true }
 
@@ -18,6 +16,6 @@ rustflags = [
   # This is a workaround to configure lints for the entire workspace, pending the ability to configure this via TOML.
   # See: `https://github.com/rust-lang/cargo/issues/5034`
   #      `https://github.com/EmbarkStudios/rust-ecosystem/issues/22#issuecomment-947011395`
-  "-Aclippy::clone_double_ref",
+  "-Asuspicious_double_ref_op",
   "-Aclippy::ptr_arg",
 ]
diff --git a/Makefile-luarocks b/Makefile-luarocks
index 7ea0dc624..c4ded991d 100644
--- a/Makefile-luarocks
+++ b/Makefile-luarocks
@@ -17,7 +17,7 @@ $(LUAMODLOCK): lua_modules $(LUAMODSPEC)
 	$(genrockslock) > $@
 else
 LUAMODLOCK :=
-LUA_PATH := $(shell lua$(LUA_VERSION) -e 'print(package.path)')
-LUA_CPATH := $(shell lua$(LUA_VERSION) -e 'print(package.cpath)')
+LUA_PATH := $(shell $(LUA) -e 'print(package.path)')
+LUA_CPATH := $(shell $(LUA) -e 'print(package.cpath)')
 export LUA_PATH LUA_CPATH
 endif
diff --git a/configure.ac b/configure.ac
index a8556081b..330d6e2fc 100644
--- a/configure.ac
+++ b/configure.ac
@@ -158,15 +158,7 @@ AM_COND_IF([DEPENDENCY_CHECKS], [
         fi
     ])
 
-    case $host_os in
-        msys)
-            LUA_VERSION=5.3 # By fiat. This is obviously not good.
-            ;;
-        *)
-            AX_PROG_LUA([5.1])
-            ;;
-    esac
-
+    AX_PROG_LUA([5.1])
     AX_LUA_HEADERS
     AX_LUA_LIBS
 
@@ -308,16 +300,23 @@ AX_SUBST_TRANSFORMED_PACKAGE_NAME
 # Avoid need for `--datarootdir=$(cd ..; pwd)` hack to run locally for
 # tests/manual build when developer mode is enabled
 AM_COND_IF([DEVELOPER], [
-        AC_DEFINE_UNQUOTED([SILE_PATH],["$(pwd)"],[Path for SILE packages and classes])
+        adl_RECURSIVE_EVAL(["$(pwd)"], [SILE_PATH])
+        AC_DEFINE_UNQUOTED([SILE_PATH], ["${SILE_PATH}"], [Path for SILE packages and classes])
+        adl_RECURSIVE_EVAL(["$(${LUA} -e 'print(package.path)')"], [LUA_PATH])
+        AC_DEFINE_UNQUOTED([LUA_PATH], ["${LUA_PATH}"],[System Lua package path])
+        adl_RECURSIVE_EVAL(["$(${LUA} -e 'print(package.cpath)')"], [LUA_CPATH])
+        AC_DEFINE_UNQUOTED([LUA_CPATH], ["${LUA_CPATH}"], [System Lua package cpath])
     ],[
         adl_RECURSIVE_EVAL(["${datadir}/${TRANSFORMED_PACKAGE_NAME}"], [SILE_PATH])
-        AC_DEFINE_UNQUOTED([SILE_PATH],["${SILE_PATH}"],[Path for SILE packages and classes])
+        AC_DEFINE_UNQUOTED([SILE_PATH], ["${SILE_PATH}"], [Path for SILE packages and classes])
 ])
 
 AC_SUBST([SILE_PATH])
+AC_SUBST([LUA_PATH])
+AC_SUBST([LUA_CPATH])
 
 adl_RECURSIVE_EVAL(["${libdir}/${TRANSFORMED_PACKAGE_NAME}"], [SILE_LIB_PATH])
-AC_DEFINE_UNQUOTED([SILE_LIB_PATH],["${SILE_LIB_PATH}"],[Path for SILE libraries])
+AC_DEFINE_UNQUOTED([SILE_LIB_PATH],["${SILE_LIB_PATH}"], [Path for SILE libraries])
 AC_SUBST([SILE_LIB_PATH])
 
 AC_SUBST([ROCKSPECWARNING], ["DO NOT EDIT! Modify template sile.rockspec.in"])
diff --git a/core/pathsetup.lua.in b/core/pathsetup.lua.in
index b9ef4bc29..413d3ce65 100644
--- a/core/pathsetup.lua.in
+++ b/core/pathsetup.lua.in
@@ -1,3 +1,9 @@
+-- Allow autoconf to setup system lua paths at compile time, not run time (only used in developer mode)
+if "@LUA_PATH@" ~= "" then
+  package.path = "@LUA_PATH@"
+  package.cpath = "@LUA_CPATH@"
+end
+
 local executable = debug.getinfo(3, "S").source
 local luaversion = _VERSION:match("%d+%.%d+")