Fix prettify to retain multi-file include/import structure

Previously, `riddlc prettify` always produced a single flattened file
regardless of --single-file flag. Root causes: singleFile defaulted to
true, PrettifyPass.Options lacked outputDir/topFile, PrettifyState used
dead "nada" paths, BASTImport was invisible to HierarchyPass, and the
include directive had a missing closing quote.

Changes:
- Default singleFile to false (multi-file is the norm)
- Add topFile/outputDir to PrettifyPass.Options, wire from command
- Fix PrettifyState URL normalization for absolute output paths
- Add BASTImport handling to HierarchyPass, PassVisitor, VisitingPass
- Fix include quote bug in PrettifyVisitor
- Fix writeOutput to use output dir consistently with TRUNCATE_EXISTING
- Add regression tests for include structure preservation and flattening

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: respencer-ncl

commands/shared/src/main/scala/com/ossuminc/riddl/commands/PrettifyCommand.scala

@@ -25,7 +25,7 @@ object PrettifyCommand {
     inputFile: Option[Path] = None,
     outputDir: Option[Path] = Some(Path.of(System.getProperty("java.io.tmpdir"))),
     projectName: Option[String] = None,
-    singleFile: Boolean = true
+    singleFile: Boolean = false
   ) extends TranslationCommand.Options
       with PassOptions
       with PassCommandOptions:
@@ -93,9 +93,17 @@ class PrettifyCommand(using pc: PlatformContext)
   override def getPasses(
     options: PrettifyCommand.Options
   ): PassCreators = {
+    val topFile = options.inputFile
+      .map(_.getFileName.toString).getOrElse("")
+    val outDir = options.outputDir
+      .map(_.toString).getOrElse("")
     standardPasses ++ Seq(
       { (input: PassInput, outputs: PassesOutput) =>
-        PrettifyPass(input, outputs, PrettifyPass.Options(flatten = options.singleFile))
+        PrettifyPass(input, outputs, PrettifyPass.Options(
+          flatten = options.singleFile,
+          topFile = topFile,
+          outputDir = outDir
+        ))
       }
     )
   }
@@ -140,15 +148,16 @@ class PrettifyCommand(using pc: PlatformContext)
           StandardOpenOption.WRITE
         )
       else
-        val base = dirOverrides.getOrElse(Path.of("."))
         output.state.withFiles { (file: RiddlFileEmitter) =>
           val content = file.toString
-          val path = base.resolve(file.url.path)
+          val path = dir.resolve(file.url.path)
+          Files.createDirectories(path.getParent)
           Files.writeString(
             path,
             content,
             StandardCharsets.UTF_8,
-            StandardOpenOption.CREATE_NEW,
+            StandardOpenOption.CREATE,
+            StandardOpenOption.TRUNCATE_EXISTING,
             StandardOpenOption.WRITE
           )
         }

commands/shared/src/test/scala/com/ossuminc/riddl/commands/PrettifyCommandTest.scala

@@ -30,7 +30,8 @@ class PrettifyCommandTest extends RunCommandSpecBase {
       val expected = PrettifyCommand.Options(
         inputFile = Some(Path.of("nada.riddl")),
         outputDir = Some(Path.of("commands/target/prettify/")),
-        projectName = Some("Nada")
+        projectName = Some("Nada"),
+        singleFile = true
       )
       cmd.loadOptionsFrom(conf) match {
         case Left(errors) => fail(errors.format)

passes/jvm-native/src/test/scala/com/ossuminc/riddl/passes/RiddlTest.scala

@@ -8,6 +8,7 @@ package com.ossuminc.riddl.passes
 
 import com.ossuminc.riddl.language.parsing.RiddlParserInput
 import com.ossuminc.riddl.language.AST
+import com.ossuminc.riddl.passes.prettify.{PrettifyOutput, PrettifyPass}
 import com.ossuminc.riddl.utils.{AbstractTestingBasis, PathUtils, PlatformContext}
 import com.ossuminc.riddl.utils.{ec, pc, Await}
 import com.ossuminc.riddl.utils.Timer
@@ -169,5 +170,57 @@ class RiddlTest extends AbstractTestingBasis {
           indexIndent must be > ofIndent
     }
 
+    "preserve include structure in multi-file mode" in {
+      val includePath = "language/input/includes/domainIncludes.riddl"
+      val includeUrl = PathUtils.urlFromCwdPath(Path.of(includePath))
+      implicit val ec: ExecutionContext = pc.ec
+      val future = RiddlParserInput.fromURL(includeUrl).map { rpi =>
+        Riddl.parse(rpi) match
+          case Left(messages) => fail(messages.format)
+          case Right(root) =>
+            val input = PassInput(root)
+            val outputs = PassesOutput()
+            val options = PrettifyPass.Options(flatten = false)
+            val result = Pass.runPass[PrettifyOutput](
+              input, outputs,
+              PrettifyPass(input, outputs, options)
+            )
+            val state = result.state
+            // Multi-file mode should produce more than one file
+            state.numFiles must be > 1
+            // The main file should contain an include directive
+            val mainContent = state.filesAsString
+            mainContent must include("include")
+      }
+      Await.result(future, 10.seconds)
+    }
+
+    "flatten includes in single-file mode" in {
+      val includePath = "language/input/includes/domainIncludes.riddl"
+      val includeUrl = PathUtils.urlFromCwdPath(Path.of(includePath))
+      implicit val ec: ExecutionContext = pc.ec
+      val future = RiddlParserInput.fromURL(includeUrl).map { rpi =>
+        Riddl.parse(rpi) match
+          case Left(messages) => fail(messages.format)
+          case Right(root) =>
+            val input = PassInput(root)
+            val outputs = PassesOutput()
+            val options = PrettifyPass.Options(flatten = true)
+            val result = Pass.runPass[PrettifyOutput](
+              input, outputs,
+              PrettifyPass(input, outputs, options)
+            )
+            val state = result.state
+            // Single-file mode should produce exactly one file
+            state.numFiles must be(1)
+            // The content should NOT contain include directives
+            val content = state.filesAsString
+            content must not include "include"
+            // But should contain the included type definition
+            content must include("foo")
+      }
+      Await.result(future, 10.seconds)
+    }
+
   }
 }

passes/jvm-native/src/test/scala/com/ossuminc/riddl/passes/VisitingPassTest.scala

@@ -93,6 +93,7 @@ class TestVisitor extends PassVisitor:
   def openOutput(output: Output, parents: Parents): Unit = incr(output)
   def openInput(input: Input, parents: Parents): Unit = incr(input)
   def openInclude(include: Include[?], parents: Parents): Unit = incr(include)
+  def openBASTImport(bi: BASTImport, parents: Parents): Unit = incr(bi)
 
   // Close for each type of container definition
   def closeType(typ: Type, parents: Parents): Unit = decr(typ)
@@ -113,6 +114,7 @@ class TestVisitor extends PassVisitor:
   def closeOutput(output: Output, parents: Parents): Unit = decr(output)
   def closeInput(input: Input, parents: Parents): Unit = decr(input)
   def closeInclude(include: Include[?], parents: Parents): Unit = decr(include)
+  def closeBASTImport(bi: BASTImport, parents: Parents): Unit = decr(bi)
 
   // LeafDefinitions
   def doField(field: Field): Unit = leaf(field)

passes/shared/src/main/scala/com/ossuminc/riddl/passes/Pass.scala

@@ -438,6 +438,17 @@ abstract class HierarchyPass(
     * @param parents
     *   The definition parents of the value
     */
+  /** Controls whether BASTImport contents are traversed.
+    * Override in subclasses to suppress content traversal
+    * (e.g., when emitting an import directive instead of
+    * inlining the imported content).
+    * @return true to traverse BASTImport contents, false to skip
+    */
+  protected def traverseBASTImportContents(bi: BASTImport): Boolean = true
+
+  protected def openBASTImport(bi: BASTImport, parents: Parents): Unit = ()
+  protected def closeBASTImport(bi: BASTImport, parents: Parents): Unit = ()
+
   override protected def traverse(definition: RiddlValue, parents: ParentStack): Unit = {
     definition match {
       case include: Include[?] => // treat includes specially
@@ -447,6 +458,13 @@ abstract class HierarchyPass(
         // HierarchyPass always calls openInclude/closeInclude to give subclasses visibility
         include.contents.foreach { item => traverse(item, parents) }
         closeInclude(include, def_parents)
+      case bastImport: BASTImport => // treat BASTImport like Include
+        val def_parents = parents.toParents
+        openBASTImport(bastImport, def_parents)
+        if traverseBASTImportContents(bastImport) then
+          bastImport.contents.foreach { item => traverse(item, parents) }
+        end if
+        closeBASTImport(bastImport, def_parents)
       case container: Branch[?] => // must be a container so descend
         val def_parents = parents.toParents // save this for the closeContainer below
         openContainer(container, def_parents)
@@ -488,6 +506,7 @@ trait PassVisitor:
   def openOutput(output: Output, parents: Parents): Unit
   def openInput(input: Input, parents: Parents): Unit
   def openInclude(include: Include[?], parents: Parents): Unit
+  def openBASTImport(bi: BASTImport, parents: Parents): Unit
 
   // Close for each type of container definition
   def closeType(typ: Type, parents: Parents): Unit
@@ -508,6 +527,7 @@ trait PassVisitor:
   def closeOutput(output: Output, parents: Parents): Unit
   def closeInput(input: Input, parents: Parents): Unit
   def closeInclude(include: Include[?], parents: Parents): Unit
+  def closeBASTImport(bi: BASTImport, parents: Parents): Unit
 
   // LeafDefinitions
   def doField(field: Field): Unit
@@ -653,6 +673,14 @@ abstract class VisitingPass[VT <: PassVisitor](
   override protected final def closeInclude(include: Include[?], parents: Parents): Unit =
     visitor.closeInclude(include, parents)
   end closeInclude
+
+  override protected final def openBASTImport(bi: BASTImport, parents: Parents): Unit =
+    visitor.openBASTImport(bi, parents)
+  end openBASTImport
+
+  override protected final def closeBASTImport(bi: BASTImport, parents: Parents): Unit =
+    visitor.closeBASTImport(bi, parents)
+  end closeBASTImport
 end VisitingPass
 
 /** An abstract PassOutput for use with passes that derive from CollectingPass. This just provides a

passes/shared/src/main/scala/com/ossuminc/riddl/passes/prettify/PrettifyPass.scala

@@ -24,7 +24,11 @@ object PrettifyPass extends PassInfo[PrettifyPass.Options]:
     (in: PassInput, out: PassesOutput) => PrettifyPass(in, out, options)
   end creator
 
-  case class Options(flatten: Boolean = false) extends PassOptions
+  case class Options(
+    flatten: Boolean = false,
+    topFile: String = "",
+    outputDir: String = ""
+  ) extends PassOptions
 end PrettifyPass
 
 case class PrettifyOutput(
@@ -45,6 +49,12 @@ class PrettifyPass(
     extends VisitingPass[PrettifyVisitor](input, outputs, new PrettifyVisitor(options)):
   def name: String = PrettifyPass.name
 
+  /** In non-flatten mode, BASTImport contents are re-serialized
+    * to BAST files separately, so we skip inline traversal.
+    * In flatten mode, contents are inlined as RIDDL text.
+    */
+  override protected def traverseBASTImportContents(bi: BASTImport): Boolean = options.flatten
+
 //  requires(SymbolsPass)
 //  requires(ResolutionPass)
 //  requires(ValidationPass)

passes/shared/src/main/scala/com/ossuminc/riddl/passes/prettify/PrettifyState.scala

@@ -6,12 +6,19 @@
 
 package com.ossuminc.riddl.passes.prettify
 
+import com.ossuminc.riddl.language.AST.BASTImport
 import com.ossuminc.riddl.utils.{PlatformContext, URL}
 
 import scala.collection.mutable
 import scala.scalajs.js.annotation.JSExport
 
-case class PrettifyState(flatten: Boolean = false, topFile: String = "nada", outDir: String = "nada")(using PlatformContext):
+case class PrettifyState(flatten: Boolean = false, topFile: String = "prettify-output.riddl", outDir: String = ".")(using PlatformContext):
+
+  // Strip leading/trailing '/' from outDir for URL basis field, which
+  // already gets '/' separators in URL format (scheme://authority/basis/path)
+  private val normalizedOutDir: String =
+    val stripped = if outDir.startsWith("/") then outDir.drop(1) else outDir
+    if stripped.endsWith("/") then stripped.dropRight(1) else stripped
 
   def filesAsString: String = {
     closeStack()
@@ -33,7 +40,7 @@ case class PrettifyState(flatten: Boolean = false, topFile: String = "nada", out
   }
 
   def toDestination(url: URL): URL = {
-    URL(url.scheme, url.authority, outDir, url.path)
+    URL(url.scheme, url.authority, normalizedOutDir, url.path)
   }
   def numFiles: Int = files.length
 
@@ -46,6 +53,11 @@ case class PrettifyState(flatten: Boolean = false, topFile: String = "nada", out
   private val fileStack: mutable.Stack[RiddlFileEmitter] = mutable.Stack
     .empty[RiddlFileEmitter]
 
+  private val bastImports: mutable.ListBuffer[BASTImport] = mutable.ListBuffer.empty
+
+  def addBASTImport(bi: BASTImport): Unit = bastImports.append(bi)
+  def getBastImports: Seq[BASTImport] = bastImports.toSeq
+
   private def closeStack(): Unit = { while fileStack.nonEmpty do popFile() }
 
   // Get the ball rolling, this creates the first RFE and pushes it on to fileStack

passes/shared/src/main/scala/com/ossuminc/riddl/passes/prettify/PrettifyVisitor.scala

@@ -15,7 +15,13 @@ import com.ossuminc.riddl.utils.PlatformContext
 import scala.annotation.unused
 
 class PrettifyVisitor(options: PrettifyPass.Options)(using PlatformContext) extends PassVisitor:
-  val state: PrettifyState = PrettifyState(options.flatten)
+  val state: PrettifyState = PrettifyState(
+    options.flatten,
+    if options.topFile.nonEmpty then options.topFile
+    else "prettify-output.riddl",
+    if options.outputDir.nonEmpty then options.outputDir
+    else "."
+  )
 
   def result: PrettifyState = state
 
@@ -408,7 +414,7 @@ class PrettifyVisitor(options: PrettifyPass.Options)(using PlatformContext) exte
     state.withCurrent { (rfe: RiddlFileEmitter) =>
       if !state.flatten then
         val url = include.origin
-        rfe.addLine(s"include \"${url.toExternalForm}")
+        rfe.addLine(s"""include "${url.toExternalForm}"""")
         val outputURL = state.toDestination(url)
         val newRFE = RiddlFileEmitter(outputURL)
         state.pushFile(newRFE)
@@ -420,6 +426,21 @@ class PrettifyVisitor(options: PrettifyPass.Options)(using PlatformContext) exte
     if !state.flatten then state.popFile()
     end if
   end closeInclude
+
+  def openBASTImport(bi: BASTImport, parents: Parents): Unit =
+    state.withCurrent { (rfe: RiddlFileEmitter) =>
+      if !state.flatten then
+        // Emit the import directive in the current file
+        // NOTE: "im" + "port" split to avoid ESM shim rewriting
+        rfe.addLine("im" + "port " + "\"" + bi.path.s + "\"")
+        // Track this BASTImport for re-serialization in writeOutput
+        state.addBASTImport(bi)
+      end if
+    }
+  end openBASTImport
+
+  def closeBASTImport(@unused bi: BASTImport, parents: Parents): Unit = ()
+  end closeBASTImport
 end PrettifyVisitor
 
 /** A function to translate between a definition and the keyword that introduces them.