diff --git a/PKGMETA.yml b/PKGMETA.yml
index af2fd7ed237..a691c721c24 100644
--- a/PKGMETA.yml
+++ b/PKGMETA.yml
@@ -83,9 +83,6 @@ packages:
   colormake-git:
     references:
       archlinux: ~
-  gnu-netcat:
-    references:
-      cygwin: ~
   mingw-w64-cross-tools:
     references:
       # doesn't exist, this is the next best thing
@@ -103,11 +100,6 @@ packages:
   mingw-w64-cross-headers:
     references:
       archlinux: mingw-w64-headers
-  libtre-git:
-    references:
-      archlinux: tre
-  autotools:
-    internal: true
   mingw-w64-cross-clang-crt:
     references:
       archlinux: mingw-w64-crt
diff --git a/autotools/PKGBUILD b/autotools/PKGBUILD
index d1965e8ba16..5b0bef0881a 100644
--- a/autotools/PKGBUILD
+++ b/autotools/PKGBUILD
@@ -15,5 +15,6 @@ depends=(
   'make'
   'pkgconf'
 )
+msys2_internal=true
 source=(README.md)
 sha256sums=('de6ec37dee4875be8e2759dea340f6c1bbdc04457333dc666dcb81b00962a145')
diff --git a/gnu-netcat/PKGBUILD b/gnu-netcat/PKGBUILD
index 50245d48ca7..f8a70d52404 100644
--- a/gnu-netcat/PKGBUILD
+++ b/gnu-netcat/PKGBUILD
@@ -16,6 +16,9 @@ source=("https://downloads.sourceforge.net/sourceforge/netcat/netcat-$pkgver.tar
         gnu-netcat-0.7.1-msys2.patch)
 sha256sums=('b55af0bbdf5acc02d1eb6ab18da2acd77a400bafd074489003f3df09676332bb'
             'b393ccc367a14bc2b48049c5ad668fade37fc32a4d8fcf47df9f0721923c02fc')
+msys2_references=(
+  'cygwin'
+)
 
 prepare() {
   cd "${srcdir}/netcat-${pkgver}"
diff --git a/libtre-git/PKGBUILD b/libtre-git/PKGBUILD
index 3d4e62649b1..55cae27a363 100644
--- a/libtre-git/PKGBUILD
+++ b/libtre-git/PKGBUILD
@@ -15,6 +15,9 @@ makedepends=("gettext-devel" "libiconv-devel" "gcc" "git" 'autotools')
 _commit="6fb7206b935b35814c5078c20046dbe065435363"
 source=("${pkgname}"::"git+https://github.com/laurikari/tre#commit=${_commit}")
 sha256sums=('SKIP')
+msys2_references=(
+  'archlinux: tre'
+)
 
 pkgver() {
   cd "${srcdir}/${pkgname}"