handle duplicated protos in include paths with ScalaPB-Options-Proto

> .../bottom/target/protobuf_external/validate/scalapb-options.proto":
> Input is shadowed in the --proto_path by
> ".../top/target/protobuf_external/validate/scalapb-options.proto".
> Either use the latter file as your input or reorder the --proto_path
> so that the former file's location comes first.

src/main/scala/sbtprotoc/ProtocPlugin.scala

@@ -305,8 +305,8 @@ object ProtocPlugin extends AutoPlugin {
       PB.includePaths := (
         PB.includePaths.?.value.getOrElse(Nil) ++
           PB.protoSources.value ++
-          protocIncludeDependencies.value ++
-          Seq(PB.externalIncludePath.value, PB.externalSourcePath.value),
+          Seq(PB.externalIncludePath.value, PB.externalSourcePath.value) ++
+          protocIncludeDependencies.value,
       ).distinct,
       PB.generate := sourceGeneratorTask(PB.generate)
         .dependsOn(

src/sbt-test/integration/common-protos/bottom/src/main/protobuf/test2.proto

@@ -0,0 +1,7 @@
+syntax = "proto3";
+
+import "validate/validate.proto";
+
+message Bar {
+    validate.Int32Rules rules = 1;
+}

src/sbt-test/integration/common-protos/build.sbt

@@ -1,10 +1,17 @@
-import scalapb.compiler.Version.protobufVersion
+ThisBuild / scalaVersion := "2.13.4"
 
-scalaVersion := "2.13.4"
+lazy val top = (project in file("top"))
+  .settings(commonSettings)
 
-Compile / PB.targets := Seq(scalapb.gen(flatPackage=true) -> (Compile / sourceManaged).value)
+lazy val bottom = (project in file("bottom"))
+  .dependsOn(top)
+  .settings(commonSettings)
 
-libraryDependencies ++= Seq(
-  "com.thesamet.scalapb.common-protos" %% "pgv-proto-scalapb_0.10" % "0.4.1-1" % "protobuf",
-  "com.thesamet.scalapb.common-protos" %% "pgv-proto-scalapb_0.10" % "0.4.1-1"
+lazy val commonSettings = Seq(
+  Compile / PB.targets := Seq(scalapb.gen(flatPackage = true) -> (Compile / sourceManaged).value),
+  libraryDependencies ++= Seq(
+    // Announcing compilation with flatPackage=false in `ScalaPB-Options-Proto`
+    "com.thesamet.scalapb.common-protos" %% "pgv-proto-scalapb_0.10" % "0.4.1-1" % "protobuf",
+    "com.thesamet.scalapb.common-protos" %% "pgv-proto-scalapb_0.10" % "0.4.1-1"
+  )
 )

src/sbt-test/integration/common-protos/test

@@ -1 +1,4 @@
-> compile
+> bottom/compile
+
+$ exists ./top/target/scala-2.13/classes/Foo.class
+$ exists ./bottom/target/scala-2.13/classes/Bar.class