isabelle: fix permission of copied files

some files are copied from the nix store and may not be writeable, so set them writeable on copy

pkgs/by-name/is/isabelle/fix-copied-permissions.patch

@@ -0,0 +1,10 @@
+--- a/src/Pure/System/isabelle_system.scala
++++ b/src/Pure/System/isabelle_system.scala
+@@ -214,6 +214,7 @@ object Isabelle_System {
+         Files.copy(src.toPath, target.toPath,
+           StandardCopyOption.COPY_ATTRIBUTES,
+           StandardCopyOption.REPLACE_EXISTING)
++        target.setWritable(true)
+       }
+       catch {
+         case ERROR(msg) =>

pkgs/by-name/is/isabelle/package.nix

@@ -119,6 +119,12 @@ stdenv.mkDerivation (finalAttrs: {
     net-tools
   ];
 
+  patches = [
+    # Make "isabelle build" work when generating documents
+    # See: https://github.com/NixOS/nixpkgs/issues/289529
+    ./fix-copied-permissions.patch
+  ];
+
   propagatedBuildInputs = lib.optionals stdenv.hostPlatform.isDarwin [ procps ];
 
   sourceRoot = "${finalAttrs.dirname}${lib.optionalString stdenv.hostPlatform.isDarwin ".app"}";