diff --git a/modules/build/src/main/scala/scala/build/bsp/BspClient.scala b/modules/build/src/main/scala/scala/build/bsp/BspClient.scala
index 59346d8add..1302a774bd 100644
--- a/modules/build/src/main/scala/scala/build/bsp/BspClient.scala
+++ b/modules/build/src/main/scala/scala/build/bsp/BspClient.scala
@@ -202,8 +202,8 @@ class BspClient(
         }
       }
         .groupBy(_.positions.headOption match
-          case Some(File(Right(path), _, _)) => Some(path)
-          case _                             => None
+          case Some(File(Right(path), _, _, _)) => Some(path)
+          case _                                => None
         )
         .filter(_._1.isDefined)
         .values
@@ -222,7 +222,7 @@ class BspClient(
     reset: Boolean = false
   )(diag: Diagnostic): Seq[os.Path] =
     diag.positions.flatMap {
-      case File(Right(path), (startLine, startC), (endL, endC)) =>
+      case File(Right(path), (startLine, startC), (endL, endC), _) =>
         val id       = new b.TextDocumentIdentifier(path.toNIO.toUri.toASCIIString)
         val startPos = new b.Position(startLine, startC)
         val endPos   = new b.Position(endL, endC)
diff --git a/modules/build/src/main/scala/scala/build/preprocessing/DirectivesPreprocessor.scala b/modules/build/src/main/scala/scala/build/preprocessing/DirectivesPreprocessor.scala
index 1fc600d258..6a493ed232 100644
--- a/modules/build/src/main/scala/scala/build/preprocessing/DirectivesPreprocessor.scala
+++ b/modules/build/src/main/scala/scala/build/preprocessing/DirectivesPreprocessor.scala
@@ -133,7 +133,7 @@ case class DirectivesPreprocessor(
 
     val handlersMap = handlers
       .flatMap { handler =>
-        handler.keys.map(k => k -> handleValues(handler))
+        handler.keys.flatMap(_.nameAliases).map(k => k -> handleValues(handler))
       }
       .toMap
 
diff --git a/modules/build/src/main/scala/scala/build/preprocessing/ExtractedDirectives.scala b/modules/build/src/main/scala/scala/build/preprocessing/ExtractedDirectives.scala
index 4f4846ec0f..d9ce4ef21d 100644
--- a/modules/build/src/main/scala/scala/build/preprocessing/ExtractedDirectives.scala
+++ b/modules/build/src/main/scala/scala/build/preprocessing/ExtractedDirectives.scala
@@ -53,8 +53,9 @@ object ExtractedDirectives {
 
       val directivesOpt = allDirectives.headOption
       val directivesPositionOpt = directivesOpt match {
-        case Some(directives) if directives.containsTargetDirectivesOnly =>
-          None
+        case Some(directives)
+            if directives.containsTargetDirectives ||
+            directives.isEmpty => None
         case Some(directives) => Some(directives.getPosition(path))
         case None             => None
       }
diff --git a/modules/build/src/main/scala/scala/build/preprocessing/ScalaPreprocessor.scala b/modules/build/src/main/scala/scala/build/preprocessing/ScalaPreprocessor.scala
index a46e12c212..3e4ced4fd1 100644
--- a/modules/build/src/main/scala/scala/build/preprocessing/ScalaPreprocessor.scala
+++ b/modules/build/src/main/scala/scala/build/preprocessing/ScalaPreprocessor.scala
@@ -240,7 +240,9 @@ case object ScalaPreprocessor extends Preprocessor {
       val summedOptions      = allOptions.foldLeft(BuildOptions())(_ orElse _)
       val lastContentOpt = preprocessedDirectives.strippedContent
         .orElse(if (isSheBang) Some(content0) else None)
-      val directivesPositions = preprocessedDirectives.directivesPositions
+      val directivesPositions = preprocessedDirectives.directivesPositions.map { pos =>
+        if (isSheBang) pos.copy(endPos = pos.endPos._1 + 1 -> pos.endPos._2) else pos
+      }
 
       val scopedRequirements = preprocessedDirectives.scopedReqs
       Some(ProcessingOutput(
diff --git a/modules/build/src/main/scala/scala/build/preprocessing/ScriptPreprocessor.scala b/modules/build/src/main/scala/scala/build/preprocessing/ScriptPreprocessor.scala
index 3cb7bf3f59..89bddc4e72 100644
--- a/modules/build/src/main/scala/scala/build/preprocessing/ScriptPreprocessor.scala
+++ b/modules/build/src/main/scala/scala/build/preprocessing/ScriptPreprocessor.scala
@@ -85,14 +85,11 @@ case object ScriptPreprocessor extends Preprocessor {
     suppressWarningOptions: SuppressWarningOptions
   )(using ScalaCliInvokeData): Either[BuildException, List[PreprocessedSource.UnwrappedScript]] =
     either {
-
-      val (contentIgnoredSheBangLines, _) = SheBang.ignoreSheBangLines(content)
-
       val (pkg, wrapper) = AmmUtil.pathToPackageWrapper(subPath)
 
       val processingOutput: ProcessingOutput =
         value(ScalaPreprocessor.process(
-          contentIgnoredSheBangLines,
+          content,
           reportingPath,
           scopePath / os.up,
           logger,
@@ -102,7 +99,8 @@ case object ScriptPreprocessor extends Preprocessor {
         ))
           .getOrElse(ProcessingOutput.empty)
 
-      val scriptCode = processingOutput.updatedContent.getOrElse(contentIgnoredSheBangLines)
+      val scriptCode =
+        processingOutput.updatedContent.getOrElse(SheBang.ignoreSheBangLines(content)._1)
       // try to match in multiline mode, don't match comment lines starting with '//'
       val containsMainAnnot = "(?m)^(?!//).*@main.*".r.findFirstIn(scriptCode).isDefined
 
diff --git a/modules/build/src/main/scala/scala/build/preprocessing/SheBang.scala b/modules/build/src/main/scala/scala/build/preprocessing/SheBang.scala
index 3b1b29fb56..a8ea735faa 100644
--- a/modules/build/src/main/scala/scala/build/preprocessing/SheBang.scala
+++ b/modules/build/src/main/scala/scala/build/preprocessing/SheBang.scala
@@ -7,6 +7,19 @@ object SheBang {
 
   def isShebangScript(content: String): Boolean = sheBangRegex.unanchored.matches(content)
 
+  /** Returns the shebang section and the content without the shebang section */
+  def partitionOnShebangSection(content: String): (String, String) =
+    if (content.startsWith("#!")) {
+      val regexMatch = sheBangRegex.findFirstMatchIn(content)
+      regexMatch match {
+        case Some(firstMatch) =>
+          (firstMatch.toString(), content.replaceFirst(firstMatch.toString(), ""))
+        case None => ("", content)
+      }
+    }
+    else
+      ("", content)
+
   def ignoreSheBangLines(content: String): (String, Boolean) =
     if (content.startsWith("#!")) {
       val regexMatch = sheBangRegex.findFirstMatchIn(content)
diff --git a/modules/build/src/main/scala/scala/build/preprocessing/UsingDirectivesOps.scala b/modules/build/src/main/scala/scala/build/preprocessing/UsingDirectivesOps.scala
index c9481eb66b..c8d8b0e2de 100644
--- a/modules/build/src/main/scala/scala/build/preprocessing/UsingDirectivesOps.scala
+++ b/modules/build/src/main/scala/scala/build/preprocessing/UsingDirectivesOps.scala
@@ -1,20 +1,45 @@
 package scala.build.preprocessing
 
 import com.virtuslab.using_directives.custom.model.UsingDirectives
-import com.virtuslab.using_directives.custom.utils.ast.UsingDefs
+import com.virtuslab.using_directives.custom.utils.ast.*
 
+import scala.annotation.tailrec
 import scala.build.Position
 import scala.jdk.CollectionConverters.*
 
 object UsingDirectivesOps {
   extension (ud: UsingDirectives) {
     def keySet: Set[String] = ud.getFlattenedMap.keySet().asScala.map(_.toString).toSet
-    def containsTargetDirectivesOnly: Boolean = ud.keySet.forall(_.toString.startsWith("target."))
+    def containsTargetDirectives: Boolean = ud.keySet.exists(_.startsWith("target."))
 
     def getPosition(path: Either[String, os.Path]): Position.File =
-      val line   = ud.getAst().getPosition().getLine()
-      val column = ud.getAst().getPosition().getColumn()
-      Position.File(path, (0, 0), (line, column))
+      extension (pos: Positioned) {
+        def getLine   = pos.getPosition.getLine
+        def getColumn = pos.getPosition.getColumn
+      }
+
+      @tailrec
+      def getEndPostion(ast: UsingTree): (Int, Int) = ast match {
+        case uds: UsingDefs => uds.getUsingDefs.asScala match {
+            case _ :+ lastUsingDef => getEndPostion(lastUsingDef)
+            case _                 => (uds.getLine, uds.getColumn)
+          }
+        case ud: UsingDef => getEndPostion(ud.getValue)
+        case uvs: UsingValues => uvs.getValues.asScala match {
+            case _ :+ lastUsingValue => getEndPostion(lastUsingValue)
+            case _                   => (uvs.getLine, uvs.getColumn)
+          }
+        case sl: StringLiteral => (
+            sl.getLine,
+            sl.getColumn + sl.getValue.length + { if sl.getIsWrappedDoubleQuotes then 2 else 0 }
+          )
+        case bl: BooleanLiteral => (bl.getLine, bl.getColumn + bl.getValue.toString.length)
+        case el: EmptyLiteral   => (el.getLine, el.getColumn)
+      }
+
+      val (line, column) = getEndPostion(ud.getAst)
+
+      Position.File(path, (0, 0), (line, column), ud.getCodeOffset)
 
     def getDirectives =
       ud.getAst match {
@@ -24,6 +49,7 @@ object UsingDirectivesOps {
           Nil
       }
 
-    def nonEmpty: Boolean = !ud.getFlattenedMap.isEmpty
+    def nonEmpty: Boolean = !isEmpty
+    def isEmpty: Boolean  = ud.getFlattenedMap.isEmpty
   }
 }
diff --git a/modules/build/src/test/scala/scala/build/tests/DirectiveTests.scala b/modules/build/src/test/scala/scala/build/tests/DirectiveTests.scala
index e6b28e80b6..d69f92ba17 100644
--- a/modules/build/src/test/scala/scala/build/tests/DirectiveTests.scala
+++ b/modules/build/src/test/scala/scala/build/tests/DirectiveTests.scala
@@ -60,8 +60,8 @@ class DirectiveTests extends munit.FunSuite {
         assert(position.nonEmpty)
 
         val (startPos, endPos) = position.get match {
-          case Position.File(_, startPos, endPos) => (startPos, endPos)
-          case _                                  => sys.error("cannot happen")
+          case Position.File(_, startPos, endPos, _) => (startPos, endPos)
+          case _                                     => sys.error("cannot happen")
         }
 
         expect(startPos == (0, 15))
diff --git a/modules/build/src/test/scala/scala/build/tests/ScalaPreprocessorTests.scala b/modules/build/src/test/scala/scala/build/tests/ScalaPreprocessorTests.scala
index 8996117fae..87f5230799 100644
--- a/modules/build/src/test/scala/scala/build/tests/ScalaPreprocessorTests.scala
+++ b/modules/build/src/test/scala/scala/build/tests/ScalaPreprocessorTests.scala
@@ -2,44 +2,49 @@ package scala.build.tests
 
 import com.eed3si9n.expecty.Expecty.expect
 
-import scala.build.input.{ScalaCliInvokeData, SourceScalaFile}
+import scala.build.input.{ScalaCliInvokeData, Script, SourceScalaFile}
 import scala.build.options.SuppressWarningOptions
-import scala.build.preprocessing.{PreprocessedSource, ScalaPreprocessor}
+import scala.build.preprocessing.{PreprocessedSource, ScalaPreprocessor, ScriptPreprocessor}
 
 class ScalaPreprocessorTests extends munit.FunSuite {
 
   test("should respect using directives in a .scala file with the shebang line") {
+    val lastUsingLine =
+      "//> using dep \"com.lihaoyi::os-lib::0.8.1\" \"com.lihaoyi::os-lib::0.8.1\""
     TestInputs(os.rel / "Main.scala" ->
-      """#!/usr/bin/env -S scala-cli shebang
-        |//> using dep "com.lihaoyi::os-lib::0.8.1"
-        |
-        |object Main {
-        |  def main(args: Array[String]): Unit = {
-        |    println(os.pwd)
-        |  }
-        |}""".stripMargin).fromRoot { root =>
+      s"""#!/usr/bin/env -S scala-cli shebang
+         |//> using jvm 11
+         |$lastUsingLine
+         |
+         |object Main {
+         |  def main(args: Array[String]): Unit = {
+         |    println(os.pwd)
+         |  }
+         |}""".stripMargin).fromRoot { root =>
       val scalaFile = SourceScalaFile(root, os.sub / "Main.scala")
       val Some(Right(result)) = ScalaPreprocessor.preprocess(
         scalaFile,
         logger = TestLogger(),
-        allowRestrictedFeatures = false,
+        allowRestrictedFeatures = true,
         suppressWarningOptions = SuppressWarningOptions()
       )(using ScalaCliInvokeData.dummy)
       expect(result.nonEmpty)
       val Some(directivesPositions) = result.head.directivesPositions
       expect(directivesPositions.startPos == 0 -> 0)
-      expect(directivesPositions.endPos == 3   -> 0)
+      expect(directivesPositions.endPos == 3   -> lastUsingLine.length)
     }
   }
 
   test("should respect using directives in a .sc file with the shebang line") {
+    val depLine = "//> using dep com.lihaoyi::os-lib::0.8.1"
+
     TestInputs(os.rel / "sample.sc" ->
-      """#!/usr/bin/env -S scala-cli shebang
-        |//> using dep "com.lihaoyi::os-lib::0.8.1"
-        |println(os.pwd)
-        |""".stripMargin).fromRoot { root =>
-      val scalaFile = SourceScalaFile(root, os.sub / "sample.sc")
-      val Some(Right(result)) = ScalaPreprocessor.preprocess(
+      s"""#!/usr/bin/env -S scala-cli shebang
+         |$depLine
+         |println(os.pwd)
+         |""".stripMargin).fromRoot { root =>
+      val scalaFile = Script(root, os.sub / "sample.sc", None)
+      val Some(Right(result)) = ScriptPreprocessor.preprocess(
         scalaFile,
         logger = TestLogger(),
         allowRestrictedFeatures = false,
@@ -48,7 +53,40 @@ class ScalaPreprocessorTests extends munit.FunSuite {
       expect(result.nonEmpty)
       val Some(directivesPositions) = result.head.directivesPositions
       expect(directivesPositions.startPos == 0 -> 0)
-      expect(directivesPositions.endPos == 2   -> 0)
+      expect(directivesPositions.endPos == 2   -> depLine.length)
     }
   }
+
+  val lastUsingLines = Seq(
+    "//> using dep \"com.lihaoyi::os-lib::0.8.1\" \"com.lihaoyi::os-lib::0.8.1\"" -> "string literal",
+    "//> using scala 2.13.7"       -> "numerical string",
+    "//> using objectWrapper true" -> "boolean literal",
+    "//> using objectWrapper"      -> "empty value literal"
+  )
+
+  for ((lastUsingLine, typeName) <- lastUsingLines) do
+    test(s"correct directive positions with $typeName") {
+      TestInputs(os.rel / "Main.scala" ->
+        s"""#!/usr/bin/env -S scala-cli shebang
+           |//> using jvm 11
+           |$lastUsingLine
+           |
+           |object Main {
+           |  def main(args: Array[String]): Unit = {
+           |    println(os.pwd)
+           |  }
+           |}""".stripMargin).fromRoot { root =>
+        val scalaFile = SourceScalaFile(root, os.sub / "Main.scala")
+        val Some(Right(result)) = ScalaPreprocessor.preprocess(
+          scalaFile,
+          logger = TestLogger(),
+          allowRestrictedFeatures = true,
+          suppressWarningOptions = SuppressWarningOptions()
+        )(using ScalaCliInvokeData.dummy)
+        expect(result.nonEmpty)
+        val Some(directivesPositions) = result.head.directivesPositions
+        expect(directivesPositions.startPos == 0 -> 0)
+        expect(directivesPositions.endPos == 3   -> lastUsingLine.length)
+      }
+    }
 }
diff --git a/modules/cli/src/main/scala/scala/cli/ScalaCliCommands.scala b/modules/cli/src/main/scala/scala/cli/ScalaCliCommands.scala
index c5c05f3802..f60a719d21 100644
--- a/modules/cli/src/main/scala/scala/cli/ScalaCliCommands.scala
+++ b/modules/cli/src/main/scala/scala/cli/ScalaCliCommands.scala
@@ -38,6 +38,7 @@ class ScalaCliCommands(
     directories.Directories,
     doc.Doc,
     export0.Export,
+    fix.Fix,
     fmt.Fmt,
     new HelpCmd(help),
     installcompletions.InstallCompletions,
diff --git a/modules/cli/src/main/scala/scala/cli/commands/fix/Fix.scala b/modules/cli/src/main/scala/scala/cli/commands/fix/Fix.scala
new file mode 100644
index 0000000000..3f42d6bb00
--- /dev/null
+++ b/modules/cli/src/main/scala/scala/cli/commands/fix/Fix.scala
@@ -0,0 +1,366 @@
+package scala.cli.commands.fix
+
+import caseapp.core.RemainingArgs
+
+import scala.build.Ops.EitherMap2
+import scala.build.errors.{BuildException, CompositeBuildException}
+import scala.build.input.*
+import scala.build.internal.Constants
+import scala.build.options.{BuildOptions, Scope, SuppressWarningOptions}
+import scala.build.preprocessing.directives.*
+import scala.build.preprocessing.{ExtractedDirectives, SheBang}
+import scala.build.{CrossSources, Logger, Position, Sources}
+import scala.cli.commands.shared.SharedOptions
+import scala.cli.commands.{ScalaCommand, SpecificationLevel}
+import scala.collection.immutable.HashMap
+import scala.util.chaining.scalaUtilChainingOps
+
+object Fix extends ScalaCommand[FixOptions] {
+  override def group                   = "Main"
+  override def scalaSpecificationLevel = SpecificationLevel.EXPERIMENTAL
+  override def sharedOptions(options: FixOptions): Option[SharedOptions] = Some(options.shared)
+
+  lazy val targetDirectivesKeysSet = DirectivesPreprocessingUtils.requireDirectiveHandlers
+    .flatMap(_.keys.flatMap(_.nameAliases)).toSet
+  lazy val usingDirectivesKeysGrouped = DirectivesPreprocessingUtils.usingDirectiveHandlers
+    .flatMap(_.keys)
+  lazy val usingDirectivesWithTestPrefixKeysGrouped =
+    DirectivesPreprocessingUtils.usingDirectiveWithReqsHandlers
+      .flatMap(_.keys)
+
+  val newLine = System.lineSeparator()
+
+  override def runCommand(options: FixOptions, args: RemainingArgs, logger: Logger): Unit = {
+    val inputs = options.shared.inputs(args.remaining, () => Inputs.default()).orExit(logger)
+
+    val (mainSources, testSources) = getProjectSources(inputs)
+      .left.map(CompositeBuildException(_))
+      .orExit(logger)
+
+    // Only initial inputs are used, new inputs discovered during processing of
+    // CrossSources.forInput may be shared between projects
+    val writableInputs: Seq[OnDisk] = inputs.flattened()
+      .collect { case onDisk: OnDisk => onDisk }
+
+    def isExtractedFromWritableInput(position: Option[Position.File]): Boolean = {
+      val originOrPathOpt = position.map(_.path)
+      originOrPathOpt match {
+        case Some(Right(path)) => writableInputs.exists(_.path == path)
+        case _                 => false
+      }
+    }
+
+    val projectFileContents = new StringBuilder()
+
+    given LoggingUtilities(logger, inputs.workspace)
+
+    // Deal with directives from the Main scope
+    val (directivesFromWritableMainInputs, testDirectivesFromMain) = {
+      val originalMainDirectives = getExtractedDirectives(mainSources)
+        .filterNot(hasTargetDirectives)
+
+      val transformedMainDirectives = unifyCorrespondingNameAliases(originalMainDirectives)
+
+      val allDirectives = for {
+        transformedMainDirective <- transformedMainDirectives
+        directive                <- transformedMainDirective.directives
+      } yield directive
+
+      val (testScopeDirectives, allMainDirectives) =
+        allDirectives.partition(_.key.startsWith("test"))
+
+      createFormattedLinesAndAppend(allMainDirectives, projectFileContents, isTest = false)
+
+      (
+        transformedMainDirectives.filter(d => isExtractedFromWritableInput(d.positions)),
+        testScopeDirectives
+      )
+    }
+
+    // Deal with directives from the Test scope
+    val directivesFromWritableTestInputs: Seq[TransformedTestDirectives] =
+      if (
+        testSources.paths.nonEmpty || testSources.inMemory.nonEmpty || testDirectivesFromMain.nonEmpty
+      ) {
+        val originalTestDirectives = getExtractedDirectives(testSources)
+          .filterNot(hasTargetDirectives)
+
+        val transformedTestDirectives = unifyCorrespondingNameAliases(originalTestDirectives)
+          .pipe(maybeTransformIntoTestEquivalent)
+
+        val allDirectives = for {
+          directivesWithTestPrefix <- transformedTestDirectives.map(_.withTestPrefix)
+          directive                <- directivesWithTestPrefix ++ testDirectivesFromMain
+        } yield directive
+
+        createFormattedLinesAndAppend(allDirectives, projectFileContents, isTest = true)
+
+        transformedTestDirectives
+          .filter(ttd => isExtractedFromWritableInput(ttd.positions))
+      }
+      else Seq(TransformedTestDirectives(Nil, Nil, None))
+
+    projectFileContents.append(newLine)
+
+    // Write extracted directives to project.scala
+    logger.message(s"Writing ${Constants.projectFileName}")
+    os.write.over(inputs.workspace / Constants.projectFileName, projectFileContents.toString)
+
+    def isProjectFile(position: Option[Position.File]): Boolean =
+      position.exists(_.path.contains(inputs.workspace / Constants.projectFileName))
+
+    // Remove directives from their original files, skip the project.scala file
+    directivesFromWritableMainInputs
+      .filterNot(e => isProjectFile(e.positions))
+      .foreach(d => removeDirectivesFrom(d.positions))
+    directivesFromWritableTestInputs
+      .filterNot(ttd => isProjectFile(ttd.positions))
+      .foreach(ttd => removeDirectivesFrom(ttd.positions, toKeep = ttd.noTestPrefixAvailable))
+  }
+
+  def getProjectSources(inputs: Inputs): Either[::[BuildException], (Sources, Sources)] = {
+    val buildOptions = BuildOptions()
+
+    val (crossSources, _) = CrossSources.forInputs(
+      inputs,
+      preprocessors = Sources.defaultPreprocessors(
+        buildOptions.archiveCache,
+        buildOptions.internal.javaClassNameVersionOpt,
+        () => buildOptions.javaHome().value.javaCommand
+      ),
+      logger = logger,
+      suppressWarningOptions = SuppressWarningOptions.suppressAll,
+      exclude = buildOptions.internal.exclude
+    ).orExit(logger)
+
+    val sharedOptions = crossSources.sharedOptions(buildOptions)
+    val scopedSources = crossSources.scopedSources(sharedOptions).orExit(logger)
+
+    val mainSources = scopedSources.sources(Scope.Main, sharedOptions, inputs.workspace)
+    val testSources = scopedSources.sources(Scope.Test, sharedOptions, inputs.workspace)
+
+    (mainSources, testSources).traverseN
+  }
+
+  def getExtractedDirectives(sources: Sources)(
+    using loggingUtilities: LoggingUtilities
+  ): Seq[ExtractedDirectives] = {
+    val logger = loggingUtilities.logger
+
+    val fromPaths = sources.paths.map { (path, _) =>
+      val (_, content) = SheBang.partitionOnShebangSection(os.read(path))
+      logger.debug(s"Extracting directives from ${loggingUtilities.relativePath(path)}")
+      ExtractedDirectives.from(content.toCharArray, Right(path), logger, _ => None).orExit(logger)
+    }
+
+    val fromInMemory = sources.inMemory.map { inMem =>
+      val originOrPath = inMem.originalPath.map((_, path) => path)
+      val content = originOrPath match {
+        case Right(path) =>
+          logger.debug(s"Extracting directives from ${loggingUtilities.relativePath(path)}")
+          os.read(path)
+        case Left(origin) =>
+          logger.debug(s"Extracting directives from $origin")
+          inMem.wrapperParamsOpt match {
+            // In case of script snippets, we need to drop the top wrapper lines
+            case Some(wrapperParams) => String(inMem.content)
+                .linesWithSeparators
+                .drop(wrapperParams.topWrapperLineCount)
+                .mkString
+            case None => String(inMem.content)
+          }
+      }
+
+      val (_, contentWithNoShebang) = SheBang.partitionOnShebangSection(content)
+
+      ExtractedDirectives.from(
+        contentWithNoShebang.toCharArray,
+        originOrPath,
+        logger,
+        _ => None
+      ).orExit(logger)
+    }
+
+    fromPaths ++ fromInMemory
+  }
+
+  def hasTargetDirectives(extractedDirectives: ExtractedDirectives): Boolean = {
+    // Filter out all elements that contain using target directives
+    val directivesInElement = extractedDirectives.directives.map(_.key)
+    directivesInElement.exists(key => targetDirectivesKeysSet.contains(key))
+  }
+
+  def unifyCorrespondingNameAliases(extractedDirectives: Seq[ExtractedDirectives]) =
+    extractedDirectives.map { extracted =>
+      // All keys that we migrate, not all in general
+      val allKeysGrouped   = usingDirectivesKeysGrouped ++ usingDirectivesWithTestPrefixKeysGrouped
+      val strictDirectives = extracted.directives
+
+      val strictDirectivesWithNewKeys = strictDirectives.flatMap { strictDir =>
+        val newKeyOpt = allKeysGrouped.find(_.nameAliases.contains(strictDir.key))
+          .flatMap(_.nameAliases.headOption)
+          .map { key =>
+            if (key.startsWith("test"))
+              val withTestStripped = key.stripPrefix("test").stripPrefix(".")
+              "test." + withTestStripped.take(1).toLowerCase + withTestStripped.drop(1)
+            else
+              key
+          }
+
+        newKeyOpt.map(newKey => strictDir.copy(key = newKey))
+      }
+
+      extracted.copy(directives = strictDirectivesWithNewKeys)
+    }
+
+  /** Transforms directives into their 'test.' equivalent if it exists
+    *
+    * @param extractedDirectives
+    * @return
+    *   an instance of TransformedTestDirectives containing transformed directives and those that
+    *   could not be transformed since they have no 'test.' equivalent
+    */
+  def maybeTransformIntoTestEquivalent(extractedDirectives: Seq[ExtractedDirectives])
+    : Seq[TransformedTestDirectives] =
+    for {
+      extractedFromSingleElement <- extractedDirectives
+      directives = extractedFromSingleElement.directives
+    } yield {
+      val (withTestEquivalent, noTestEquivalent) = directives.partition { directive =>
+        usingDirectivesWithTestPrefixKeysGrouped.exists(
+          _.nameAliases.contains("test." + directive.key)
+        )
+      }
+
+      val transformedToTestEquivalents = withTestEquivalent.map {
+        case StrictDirective(key, values) => StrictDirective("test." + key, values)
+      }
+
+      TransformedTestDirectives(
+        withTestPrefix = transformedToTestEquivalents,
+        noTestPrefixAvailable = noTestEquivalent,
+        positions = extractedFromSingleElement.positions
+      )
+    }
+
+  def removeDirectivesFrom(
+    position: Option[Position.File],
+    toKeep: Seq[StrictDirective] = Nil
+  )(
+    using loggingUtilities: LoggingUtilities
+  ): Unit = {
+    position match {
+      case Some(Position.File(Right(path), _, _, offset)) =>
+        val (shebangSection, strippedContent) = SheBang.partitionOnShebangSection(os.read(path))
+
+        def ignoreOrAddNewLine(str: String) = if str.isBlank then "" else str + newLine
+
+        val keepLines = ignoreOrAddNewLine(shebangSection) + ignoreOrAddNewLine(toKeep.mkString(
+          "",
+          newLine,
+          newLine
+        ))
+        val newContents  = keepLines + strippedContent.drop(offset).stripLeading()
+        val relativePath = loggingUtilities.relativePath(path)
+
+        loggingUtilities.logger.message(s"Removing directives from $relativePath")
+        if (toKeep.nonEmpty) {
+          loggingUtilities.logger.message("  Keeping:")
+          toKeep.foreach(d => loggingUtilities.logger.message(s"    $d"))
+        }
+
+        os.write.over(path, newContents.stripLeading())
+      case _ => ()
+    }
+  }
+
+  def createFormattedLinesAndAppend(
+    strictDirectives: Seq[StrictDirective],
+    projectFileContents: StringBuilder,
+    isTest: Boolean
+  ): Unit = {
+    if (strictDirectives.nonEmpty) {
+      projectFileContents
+        .append(if (projectFileContents.nonEmpty) newLine else "")
+        .append(if isTest then "// Test" else "// Main")
+        .append(newLine)
+
+      strictDirectives
+        // group by key to merge values
+        .groupBy(_.key)
+        .map { (key, directives) =>
+          StrictDirective(key, directives.flatMap(_.values))
+        }
+        // group by key prefixes to create splits between groups
+        .groupBy(dir => (if (isTest) dir.key.stripPrefix("test.") else dir.key).takeWhile(_ != '.'))
+        .map { (_, directives) =>
+          directives.flatMap(_.explodeToStringsWithColLimit()).toSeq.sorted
+        }
+        .toSeq
+        .filter(_.nonEmpty)
+        .sortBy(_.head)(using directivesOrdering)
+        // append groups to the StringBuilder, add new lines between groups that are bigger than one line
+        .foldLeft(0) { (lastSize, directiveLines) =>
+          val newSize = directiveLines.size
+          if (lastSize > 1 || (lastSize != 0 && newSize > 1)) projectFileContents.append(newLine)
+
+          directiveLines.foreach(projectFileContents.append(_).append(newLine))
+
+          newSize
+        }
+    }
+  }
+
+  case class TransformedTestDirectives(
+    withTestPrefix: Seq[StrictDirective],
+    noTestPrefixAvailable: Seq[StrictDirective],
+    positions: Option[Position.File]
+  )
+
+  case class LoggingUtilities(
+    logger: Logger,
+    workspacePath: os.Path
+  ) {
+    def relativePath(path: os.Path) =
+      if (path.startsWith(workspacePath)) path.relativeTo(workspacePath)
+      else path
+  }
+
+  private val directivesOrdering: Ordering[String] = {
+    def directivesOrder(key: String): Int = {
+      val handlersOrder = Seq(
+        ScalaVersion.handler.keys,
+        Platform.handler.keys,
+        Jvm.handler.keys,
+        JavaHome.handler.keys,
+        ScalaNative.handler.keys,
+        ScalaJs.handler.keys,
+        ScalacOptions.handler.keys,
+        JavaOptions.handler.keys,
+        JavacOptions.handler.keys,
+        JavaProps.handler.keys,
+        MainClass.handler.keys,
+        scala.build.preprocessing.directives.Sources.handler.keys,
+        ObjectWrapper.handler.keys,
+        Toolkit.handler.keys,
+        Dependency.handler.keys
+      )
+
+      handlersOrder.zipWithIndex
+        .find(_._1.flatMap(_.nameAliases).contains(key))
+        .map(_._2)
+        .getOrElse(if key.startsWith("publish") then 20 else 15)
+    }
+
+    Ordering.by { directiveLine =>
+      val key = directiveLine
+        .stripPrefix("//> using")
+        .stripLeading()
+        .stripPrefix("test.")
+        // separate key from value
+        .takeWhile(!_.isWhitespace)
+
+      directivesOrder(key)
+    }
+  }
+}
diff --git a/modules/cli/src/main/scala/scala/cli/commands/fix/FixOptions.scala b/modules/cli/src/main/scala/scala/cli/commands/fix/FixOptions.scala
new file mode 100644
index 0000000000..a1a2400abd
--- /dev/null
+++ b/modules/cli/src/main/scala/scala/cli/commands/fix/FixOptions.scala
@@ -0,0 +1,33 @@
+package scala.cli.commands.fix
+
+import caseapp.*
+import caseapp.core.help.Help
+
+import scala.cli.ScalaCli
+import scala.cli.commands.shared.{HasSharedOptions, HelpMessages, SharedOptions}
+import scala.cli.commands.tags
+
+// format: off
+@HelpMessage(FixOptions.helpMessage, "", FixOptions.detailedHelpMessage)
+final case class FixOptions(
+  @Recurse
+    shared: SharedOptions = SharedOptions()
+) extends HasSharedOptions
+// format: on
+
+object FixOptions {
+  implicit lazy val parser: Parser[FixOptions] = Parser.derive
+  implicit lazy val help: Help[FixOptions]     = Help.derive
+
+  val cmdName             = "fix"
+  private val helpHeader  = "Perform fixes on a Scala CLI project."
+  val helpMessage: String = HelpMessages.shortHelpMessage(cmdName, helpHeader)
+  val detailedHelpMessage: String =
+    s"""$helpHeader
+       |
+       |${HelpMessages.commandConfigurations(cmdName)}
+       |
+       |${HelpMessages.acceptedInputs}
+       |
+       |${HelpMessages.commandDocWebsiteReference(cmdName)}""".stripMargin
+}
diff --git a/modules/core/src/main/scala/scala/build/Position.scala b/modules/core/src/main/scala/scala/build/Position.scala
index 250e20873e..e7a13984e8 100644
--- a/modules/core/src/main/scala/scala/build/Position.scala
+++ b/modules/core/src/main/scala/scala/build/Position.scala
@@ -15,7 +15,8 @@ object Position {
   final case class File(
     path: Either[String, os.Path],
     startPos: (Int, Int),
-    endPos: (Int, Int)
+    endPos: (Int, Int),
+    offset: Int = 0
   ) extends Position {
     def render(cwd: os.Path, sep: String): String = {
       val p = path match {
diff --git a/modules/directives/src/main/scala/scala/build/preprocessing/directives/CustomJar.scala b/modules/directives/src/main/scala/scala/build/preprocessing/directives/CustomJar.scala
index bb73a84630..8be6806bae 100644
--- a/modules/directives/src/main/scala/scala/build/preprocessing/directives/CustomJar.scala
+++ b/modules/directives/src/main/scala/scala/build/preprocessing/directives/CustomJar.scala
@@ -49,6 +49,7 @@ final case class CustomJar(
   @DirectiveName("source.jars")
   sourcesJar: DirectiveValueParser.WithScopePath[List[Positioned[String]]] =
     DirectiveValueParser.WithScopePath.empty(Nil),
+  @DirectiveName("test.sourcesJar")
   @DirectiveName("test.sources.jar")
   @DirectiveName("test.sourcesJars")
   @DirectiveName("test.sources.jars")
diff --git a/modules/directives/src/main/scala/scala/build/preprocessing/directives/Dependency.scala b/modules/directives/src/main/scala/scala/build/preprocessing/directives/Dependency.scala
index a41486137e..dbce2a1509 100644
--- a/modules/directives/src/main/scala/scala/build/preprocessing/directives/Dependency.scala
+++ b/modules/directives/src/main/scala/scala/build/preprocessing/directives/Dependency.scala
@@ -36,6 +36,7 @@ final case class Dependency(
   @DirectiveName("deps")
   @DirectiveName("dependencies")
   dependency: List[Positioned[String]] = Nil,
+  @DirectiveName("test.dependency")
   @DirectiveName("test.dep")
   @DirectiveName("test.deps")
   @DirectiveName("test.dependencies")
diff --git a/modules/directives/src/main/scala/scala/build/preprocessing/directives/DirectiveHandler.scala b/modules/directives/src/main/scala/scala/build/preprocessing/directives/DirectiveHandler.scala
index e1ef71ab77..40d782cb3c 100644
--- a/modules/directives/src/main/scala/scala/build/preprocessing/directives/DirectiveHandler.scala
+++ b/modules/directives/src/main/scala/scala/build/preprocessing/directives/DirectiveHandler.scala
@@ -37,7 +37,7 @@ trait DirectiveHandler[+T] { self =>
   final def isRestricted: Boolean   = scalaSpecificationLevel == SpecificationLevel.RESTRICTED
   final def isExperimental: Boolean = scalaSpecificationLevel == SpecificationLevel.EXPERIMENTAL
 
-  def keys: Seq[String]
+  def keys: Seq[Key]
 
   def handleValues(
     scopedDirective: ScopedDirective,
@@ -80,6 +80,9 @@ trait DirectiveHandler[+T] { self =>
 
 }
 
+/** Using directive key with all its aliases */
+case class Key(nameAliases: Seq[String])
+
 object DirectiveHandler {
 
   // from https://github.com/alexarchambault/case-app/blob/7ac9ae7cc6765df48eab27c4e35c66b00e4469a7/core/shared/src/main/scala/caseapp/core/util/CaseUtil.scala#L5-L22
@@ -315,9 +318,9 @@ object DirectiveHandler {
       }
 
     val keysValue = Expr.ofList {
-      fields0.flatMap {
+      fields0.map {
         case (sym, _) =>
-          withPrefix(Expr(sym.name)) +: namesFromAnnotations(sym)
+          Expr.ofList(withPrefix(Expr(sym.name)) +: namesFromAnnotations(sym))
       }
     }
 
@@ -429,15 +432,17 @@ object DirectiveHandler {
         def scalaSpecificationLevel = $levelValue
 
         lazy val keys = $keysValue
-          .flatMap(key =>
-            List(
-              key,
-              DirectiveHandler.pascalCaseSplit(key.toCharArray.toList)
-                .map(_.toLowerCase(Locale.ROOT))
-                .mkString("-")
-            )
-          )
-          .distinct
+          .map { nameAliases =>
+            val allAliases = nameAliases.flatMap(key =>
+              List(
+                key,
+                DirectiveHandler.pascalCaseSplit(key.toCharArray.toList)
+                  .map(_.toLowerCase(Locale.ROOT))
+                  .mkString("-")
+              )
+            ).distinct
+            Key(allAliases)
+          }
 
         def handleValues(scopedDirective: ScopedDirective, logger: Logger) =
           ${ handleValuesImpl('{ scopedDirective }, '{ logger }) }
diff --git a/modules/directives/src/main/scala/scala/build/preprocessing/directives/JavaOptions.scala b/modules/directives/src/main/scala/scala/build/preprocessing/directives/JavaOptions.scala
index 70d7e381d7..ee71cf937a 100644
--- a/modules/directives/src/main/scala/scala/build/preprocessing/directives/JavaOptions.scala
+++ b/modules/directives/src/main/scala/scala/build/preprocessing/directives/JavaOptions.scala
@@ -19,6 +19,7 @@ import scala.cli.commands.SpecificationLevel
 final case class JavaOptions(
   @DirectiveName("javaOpt")
   javaOptions: List[Positioned[String]] = Nil,
+  @DirectiveName("test.javaOptions")
   @DirectiveName("test.javaOpt")
   testJavaOptions: List[Positioned[String]] = Nil
 ) extends HasBuildOptionsWithRequirements {
diff --git a/modules/directives/src/main/scala/scala/build/preprocessing/directives/JavaProps.scala b/modules/directives/src/main/scala/scala/build/preprocessing/directives/JavaProps.scala
index 73bc35d52d..a13bdf275d 100644
--- a/modules/directives/src/main/scala/scala/build/preprocessing/directives/JavaProps.scala
+++ b/modules/directives/src/main/scala/scala/build/preprocessing/directives/JavaProps.scala
@@ -23,6 +23,7 @@ import scala.cli.commands.SpecificationLevel
 final case class JavaProps(
   @DirectiveName("javaProp")
   javaProperty: List[Positioned[String]] = Nil,
+  @DirectiveName("test.javaProperty")
   @DirectiveName("test.javaProp")
   testJavaProperty: List[Positioned[String]] = Nil
 ) extends HasBuildOptionsWithRequirements {
diff --git a/modules/directives/src/main/scala/scala/build/preprocessing/directives/JavacOptions.scala b/modules/directives/src/main/scala/scala/build/preprocessing/directives/JavacOptions.scala
index d327a01a68..e04fd74ff7 100644
--- a/modules/directives/src/main/scala/scala/build/preprocessing/directives/JavacOptions.scala
+++ b/modules/directives/src/main/scala/scala/build/preprocessing/directives/JavacOptions.scala
@@ -19,6 +19,7 @@ import scala.cli.commands.SpecificationLevel
 final case class JavacOptions(
   @DirectiveName("javacOpt")
   javacOptions: List[Positioned[String]] = Nil,
+  @DirectiveName("test.javacOptions")
   @DirectiveName("test.javacOpt")
   testJavacOptions: List[Positioned[String]] = Nil
 ) extends HasBuildOptionsWithRequirements {
diff --git a/modules/directives/src/main/scala/scala/build/preprocessing/directives/Resources.scala b/modules/directives/src/main/scala/scala/build/preprocessing/directives/Resources.scala
index 8c33029027..2b8ce000bc 100644
--- a/modules/directives/src/main/scala/scala/build/preprocessing/directives/Resources.scala
+++ b/modules/directives/src/main/scala/scala/build/preprocessing/directives/Resources.scala
@@ -25,6 +25,7 @@ final case class Resources(
   resourceDirs: DirectiveValueParser.WithScopePath[List[Positioned[String]]] =
     DirectiveValueParser.WithScopePath.empty(Nil),
   @DirectiveName("test.resourceDir")
+  @DirectiveName("test.resourceDirs")
   testResourceDirs: DirectiveValueParser.WithScopePath[List[Positioned[String]]] =
     DirectiveValueParser.WithScopePath.empty(Nil)
 ) extends HasBuildOptionsWithRequirements {
diff --git a/modules/directives/src/main/scala/scala/build/preprocessing/directives/StrictDirective.scala b/modules/directives/src/main/scala/scala/build/preprocessing/directives/StrictDirective.scala
index be4798ad8f..78b532243d 100644
--- a/modules/directives/src/main/scala/scala/build/preprocessing/directives/StrictDirective.scala
+++ b/modules/directives/src/main/scala/scala/build/preprocessing/directives/StrictDirective.scala
@@ -14,6 +14,35 @@ case class StrictDirective(
     val suffix = if validValues.isEmpty then "" else s" \"${validValues.mkString("\",  \"")}\""
     s"//> using $key$suffix"
   }
+
+  /** Checks whether the directive with the sequence of values will fit into the given column limit,
+    * if it does then the function returns the single directive with all the values. If the
+    * directive does not fit then the function explodes it into a sequence of directives with
+    * distinct values, each with a single value.
+    */
+  def explodeToStringsWithColLimit(colLimit: Int = 100): Seq[String] = {
+    val validValues = values.filter {
+      case _: EmptyValue => false
+      case _             => true
+    }
+
+    val usingKeyString = s"//> using $key"
+
+    if (validValues.isEmpty)
+      Seq(usingKeyString)
+    else {
+      val distinctValuesStrings = validValues
+        .map(v => s"\"${v.toString}\"")
+        .distinct
+        .sorted
+
+      if (distinctValuesStrings.map(_.length).sum + usingKeyString.length < colLimit)
+        Seq(s"$usingKeyString ${distinctValuesStrings.mkString(" ")}")
+      else
+        distinctValuesStrings.map(v => s"$usingKeyString $v")
+    }
+  }
+
   def stringValuesCount: Int =
     values.count {
       case _: StringValue => true
diff --git a/modules/directives/src/main/scala/scala/build/preprocessing/directives/Tests.scala b/modules/directives/src/main/scala/scala/build/preprocessing/directives/Tests.scala
index ba898915a5..8e5501df59 100644
--- a/modules/directives/src/main/scala/scala/build/preprocessing/directives/Tests.scala
+++ b/modules/directives/src/main/scala/scala/build/preprocessing/directives/Tests.scala
@@ -16,6 +16,7 @@ import scala.cli.commands.SpecificationLevel
 @DirectiveLevel(SpecificationLevel.SHOULD)
 // format: off
 final case class Tests(
+  @DirectiveName("test.framework")
   testFramework: Option[String] = None
 ) extends HasBuildOptions {
   // format: on
diff --git a/modules/integration/src/test/scala/scala/cli/integration/CompileTestDefinitions.scala b/modules/integration/src/test/scala/scala/cli/integration/CompileTestDefinitions.scala
index feca6ba033..d0b532684a 100644
--- a/modules/integration/src/test/scala/scala/cli/integration/CompileTestDefinitions.scala
+++ b/modules/integration/src/test/scala/scala/cli/integration/CompileTestDefinitions.scala
@@ -135,15 +135,17 @@ abstract class CompileTestDefinitions(val scalaVersionOpt: Option[String])
   }
 
   test(
-    "target directives in files should not produce warnings about using directives in multiple files"
+    "having target + using directives in files should not produce warnings about using directives in multiple files"
   ) {
     val inputs = TestInputs(
       os.rel / "Bar.java" ->
         """//> using target.platform "jvm"
+          |//> using jvm "17"
           |public class Bar {}
           |""".stripMargin,
       os.rel / "Foo.test.scala" ->
         """//> using target.scala.>= "2.13"
+          |//> using dep "com.lihaoyi::os-lib::0.8.1"
           |class Foo {}
           |""".stripMargin
     )
@@ -162,12 +164,10 @@ abstract class CompileTestDefinitions(val scalaVersionOpt: Option[String])
     val inputs = TestInputs(
       os.rel / "Bar.java" ->
         """//> using jvm "17"
-          |//> using target.scope "test"
           |public class Bar {}
           |""".stripMargin,
       os.rel / "Foo.scala" ->
-        """//> using target.scala.>= "2.13"
-          |//> using dep "com.lihaoyi::os-lib::0.8.1"
+        """//> using dep "com.lihaoyi::os-lib::0.8.1"
           |class Foo {}
           |""".stripMargin
     )
diff --git a/modules/integration/src/test/scala/scala/cli/integration/FixTests.scala b/modules/integration/src/test/scala/scala/cli/integration/FixTests.scala
new file mode 100644
index 0000000000..0a342d8746
--- /dev/null
+++ b/modules/integration/src/test/scala/scala/cli/integration/FixTests.scala
@@ -0,0 +1,407 @@
+package scala.cli.integration
+
+import com.eed3si9n.expecty.Expecty.expect
+
+class FixTests extends ScalaCliSuite {
+
+  override def group: ScalaCliSuite.TestGroup = ScalaCliSuite.TestGroup.First
+
+  val projectFileName = "project.scala"
+
+  val extraOptions = Seq("--suppress-experimental-feature-warning")
+
+  test("fix basic") {
+    val mainFileName = "Main.scala"
+    val inputs = TestInputs(
+      os.rel / mainFileName ->
+        s"""//> using objectWrapper
+           |//> using dep com.lihaoyi::os-lib:0.9.1 com.lihaoyi::upickle:3.1.2
+           |
+           |package com.foo.main
+           |
+           |object Main extends App {
+           |  println(os.pwd)
+           |}
+           |""".stripMargin,
+      os.rel / projectFileName ->
+        s"""//> using lib "com.lihaoyi::pprint:0.6.6"
+           |""".stripMargin
+    )
+
+    inputs.fromRoot { root =>
+
+      val fixOutput = os.proc(TestUtil.cli, "--power", "fix", ".", "-v", "-v", extraOptions)
+        .call(cwd = root, mergeErrIntoOut = true).out.trim()
+
+      assertNoDiff(
+        fixOutput,
+        """Extracting directives from Main.scala
+          |Extracting directives from project.scala
+          |Writing project.scala
+          |Removing directives from Main.scala""".stripMargin
+      )
+
+      val projectFileContents = os.read(root / projectFileName)
+      val mainFileContents    = os.read(root / mainFileName)
+
+      assertNoDiff(
+        projectFileContents,
+        """// Main
+          |//> using objectWrapper
+          |
+          |//> using dependency "com.lihaoyi::os-lib:0.9.1"
+          |//> using dependency "com.lihaoyi::pprint:0.6.6"
+          |//> using dependency "com.lihaoyi::upickle:3.1.2"
+          |
+          |""".stripMargin
+      )
+
+      assertNoDiff(
+        mainFileContents,
+        """package com.foo.main
+          |
+          |object Main extends App {
+          |  println(os.pwd)
+          |}
+          |""".stripMargin
+      )
+
+      val runProc = os.proc(TestUtil.cli, "--power", "compile", ".", extraOptions)
+        .call(cwd = root, stderr = os.Pipe)
+
+      expect(!runProc.err.trim.contains("Using directives detected in multiple files"))
+    }
+  }
+
+  test("fix script with shebang") {
+    val mainFileName = "main.sc"
+    val inputs = TestInputs(
+      os.rel / mainFileName ->
+        s"""#!/usr/bin/env -S scala-cli shebang
+           |
+           |//> using objectWrapper
+           |//> using dep com.lihaoyi::os-lib:0.9.1 com.lihaoyi::upickle:3.1.2
+           |
+           |println(os.pwd)
+           |""".stripMargin,
+      os.rel / projectFileName ->
+        s"""//> using lib "com.lihaoyi::pprint:0.6.6"
+           |""".stripMargin
+    )
+
+    inputs.fromRoot { root =>
+
+      val fixOutput = os.proc(TestUtil.cli, "--power", "fix", ".", "-v", "-v", extraOptions)
+        .call(cwd = root, mergeErrIntoOut = true).out.trim()
+
+      assertNoDiff(
+        fixOutput,
+        """Extracting directives from project.scala
+          |Extracting directives from main.sc
+          |Writing project.scala
+          |Removing directives from main.sc""".stripMargin
+      )
+
+      val projectFileContents = os.read(root / projectFileName)
+      val mainFileContents    = os.read(root / mainFileName)
+
+      assertNoDiff(
+        projectFileContents,
+        """// Main
+          |//> using objectWrapper
+          |
+          |//> using dependency "com.lihaoyi::os-lib:0.9.1"
+          |//> using dependency "com.lihaoyi::pprint:0.6.6"
+          |//> using dependency "com.lihaoyi::upickle:3.1.2"
+          |
+          |""".stripMargin
+      )
+
+      assertNoDiff(
+        mainFileContents,
+        """#!/usr/bin/env -S scala-cli shebang
+          |
+          |println(os.pwd)
+          |""".stripMargin
+      )
+
+      val runProc = os.proc(TestUtil.cli, "--power", "compile", ".", extraOptions)
+        .call(cwd = root, stderr = os.Pipe)
+
+      expect(!runProc.err.trim.contains("Using directives detected in multiple files"))
+    }
+  }
+
+  test("fix with test scope") {
+    val mainSubPath = os.rel / "src" / "Main.scala"
+    val testSubPath = os.rel / "test" / "MyTests.scala"
+    val inputs = TestInputs(
+      mainSubPath ->
+        s"""//> using objectWrapper
+           |//> using dep "com.lihaoyi::os-lib:0.9.1"
+           |
+           |//> using test.dep "org.typelevel::cats-core:2.9.0"
+           |
+           |package com.foo.main
+           |
+           |object Main extends App {
+           |  println(os.pwd)
+           |}
+           |""".stripMargin,
+      testSubPath ->
+        s"""//> using options -Xasync, -Xfatal-warnings
+           |//> using dep org.scalameta::munit::0.7.29
+           |
+           |package com.foo.test.bar
+           |
+           |class MyTests extends munit.FunSuite {
+           |  test("bar") {
+           |    assert(2 + 2 == 4)
+           |    println("Hello from " + "tests")
+           |  }
+           |}
+           |""".stripMargin,
+      os.rel / projectFileName ->
+        s"""//> using lib com.lihaoyi::pprint:0.6.6
+           |""".stripMargin
+    )
+
+    inputs.fromRoot { root =>
+
+      val fixOutput = os.proc(TestUtil.cli, "--power", "fix", ".", "-v", "-v", extraOptions)
+        .call(cwd = root, mergeErrIntoOut = true).out.trim()
+
+      assertNoDiff(
+        fixOutput,
+        """Extracting directives from project.scala
+          |Extracting directives from src/Main.scala
+          |Extracting directives from test/MyTests.scala
+          |Writing project.scala
+          |Removing directives from src/Main.scala
+          |Removing directives from test/MyTests.scala""".stripMargin
+      )
+
+      val projectFileContents = os.read(root / projectFileName)
+      val mainFileContents    = os.read(root / mainSubPath)
+      val testFileContents    = os.read(root / testSubPath)
+
+      assertNoDiff(
+        projectFileContents,
+        """// Main
+          |//> using objectWrapper
+          |//> using dependency "com.lihaoyi::os-lib:0.9.1" "com.lihaoyi::pprint:0.6.6"
+          |
+          |// Test
+          |//> using test.options "-Xasync" "-Xfatal-warnings"
+          |//> using test.dependency "org.scalameta::munit::0.7.29" "org.typelevel::cats-core:2.9.0"
+          |""".stripMargin
+      )
+
+      assertNoDiff(
+        mainFileContents,
+        """package com.foo.main
+          |
+          |object Main extends App {
+          |  println(os.pwd)
+          |}
+          |""".stripMargin
+      )
+
+      assertNoDiff(
+        testFileContents,
+        """package com.foo.test.bar
+          |
+          |class MyTests extends munit.FunSuite {
+          |  test("bar") {
+          |    assert(2 + 2 == 4)
+          |    println("Hello from " + "tests")
+          |  }
+          |}
+          |""".stripMargin
+      )
+
+      val runProc = os.proc(TestUtil.cli, "--power", "compile", ".", extraOptions)
+        .call(cwd = root, stderr = os.Pipe)
+
+      expect(!runProc.err.trim.contains("Using directives detected in multiple files"))
+    }
+  }
+
+  test("fix complex inputs") {
+    val mainSubPath = os.rel / "src" / "Main.scala"
+    val testSubPath = os.rel / "test" / "MyTests.scala"
+
+    val withUsedTargetSubPath = os.rel / "src" / "UsedTarget.scala"
+    val withUsedTargetContents =
+      s"""//> using target.scala 3.3.0
+         |//> using dep com.lihaoyi::upickle:3.1.2
+         |case class UsedTarget(x: Int)
+         |""".stripMargin
+    val withUnusedTargetSubPath = os.rel / "src" / "UnusedTarget.scala"
+    val withUnusedTargetContents =
+      s"""//> using target.scala 2.13
+         |//> using dep com.lihaoyi::upickle:3.1.2
+         |case class UnusedTarget(x: Int)
+         |""".stripMargin
+
+    val includedInputs = TestInputs(
+      os.rel / "Included.scala" ->
+        """//> using options -Werror
+          |
+          |case class Included(x: Int)
+          |""".stripMargin
+    )
+
+    includedInputs.fromRoot { includeRoot =>
+      val includePath = (includeRoot / "Included.scala").toString.replace("\\", "\\\\")
+
+      val inputs = TestInputs(
+        mainSubPath ->
+          s"""//> using platforms "jvm"
+             |//> using scala "3.3.0"
+             |//> using jvm "17"
+             |//> using objectWrapper
+             |//> using dep com.lihaoyi::os-lib:0.9.1
+             |//> using file $includePath
+             |
+             |//> using test.dep "org.typelevel::cats-core:2.9.0"
+             |
+             |package com.foo.main
+             |
+             |object Main extends App {
+             |  println(os.pwd)
+             |}
+             |""".stripMargin,
+        withUsedTargetSubPath   -> withUsedTargetContents,
+        withUnusedTargetSubPath -> withUnusedTargetContents,
+        testSubPath ->
+          s"""//> using options -Xasync, -Xfatal-warnings
+             |//> using dep "org.scalameta::munit::0.7.29"
+             |//> using scala 3.2.2
+             |
+             |package com.foo.test.bar
+             |
+             |class MyTests extends munit.FunSuite {
+             |  test("bar") {
+             |    assert(2 + 2 == 4)
+             |    println("Hello from " + "tests")
+             |  }
+             |}
+             |""".stripMargin,
+        os.rel / projectFileName ->
+          s"""//> using lib com.lihaoyi::pprint:0.6.6
+             |
+             |//> using publish.ci.password env:PUBLISH_PASSWORD
+             |//> using publish.ci.secretKey env:PUBLISH_SECRET_KEY
+             |//> using publish.ci.secretKeyPassword env:PUBLISH_SECRET_KEY_PASSWORD
+             |//> using publish.ci.user env:PUBLISH_USER
+             |""".stripMargin
+      )
+
+      inputs.fromRoot { root =>
+        val res = os.proc(
+          TestUtil.cli,
+          "--power",
+          "fix",
+          ".",
+          "--script-snippet",
+          "//> using toolkit latest",
+          "-v",
+          "-v",
+          extraOptions
+        ).call(cwd = root, stderr = os.Pipe)
+
+        assertNoDiff(
+          res.err.trim(),
+          s"""Extracting directives from project.scala
+             |Extracting directives from src/Main.scala
+             |Extracting directives from src/UsedTarget.scala
+             |Extracting directives from ${includeRoot / "Included.scala"}
+             |Extracting directives from snippet
+             |Extracting directives from test/MyTests.scala
+             |Writing project.scala
+             |Removing directives from src/Main.scala
+             |Removing directives from test/MyTests.scala
+             |  Keeping:
+             |    //> using scala "3.2.2"""".stripMargin
+        )
+
+        val projectFileContents          = os.read(root / projectFileName)
+        val mainFileContents             = os.read(root / mainSubPath)
+        val testFileContents             = os.read(root / testSubPath)
+        val withUsedTargetContentsRead   = os.read(root / withUsedTargetSubPath)
+        val withUnusedTargetContentsRead = os.read(root / withUnusedTargetSubPath)
+
+        assertNoDiff(
+          projectFileContents,
+          s"""// Main
+             |//> using scala "3.3.0"
+             |//> using platforms "jvm"
+             |//> using jvm "17"
+             |//> using options "-Werror"
+             |//> using files "$includePath"
+             |//> using objectWrapper
+             |//> using toolkit "latest"
+             |//> using dependency "com.lihaoyi::os-lib:0.9.1" "com.lihaoyi::pprint:0.6.6"
+             |
+             |//> using publish.ci.password "env:PUBLISH_PASSWORD"
+             |//> using publish.ci.secretKey "env:PUBLISH_SECRET_KEY"
+             |//> using publish.ci.secretKeyPassword "env:PUBLISH_SECRET_KEY_PASSWORD"
+             |//> using publish.ci.user "env:PUBLISH_USER"
+             |
+             |// Test
+             |//> using test.options "-Xasync" "-Xfatal-warnings"
+             |//> using test.dependency "org.scalameta::munit::0.7.29" "org.typelevel::cats-core:2.9.0"
+             |""".stripMargin
+        )
+
+        assertNoDiff(
+          mainFileContents,
+          """package com.foo.main
+            |
+            |object Main extends App {
+            |  println(os.pwd)
+            |}
+            |""".stripMargin
+        )
+
+        // Directives with no 'test.' equivalent are retained
+        assertNoDiff(
+          testFileContents,
+          """//> using scala "3.2.2"
+            |
+            |package com.foo.test.bar
+            |
+            |class MyTests extends munit.FunSuite {
+            |  test("bar") {
+            |    assert(2 + 2 == 4)
+            |    println("Hello from " + "tests")
+            |  }
+            |}
+            |""".stripMargin
+        )
+
+        assertNoDiff(withUsedTargetContents, withUsedTargetContentsRead)
+        assertNoDiff(withUnusedTargetContents, withUnusedTargetContentsRead)
+
+        val runProc = os.proc(TestUtil.cli, "--power", "compile", ".")
+          .call(cwd = root, stderr = os.Pipe)
+
+        val runErrOut = TestUtil.removeAnsiColors(runProc.err.trim)
+        expect(runErrOut.contains("Using directives detected in multiple files"))
+        expect(runErrOut.linesIterator.count(_.startsWith("[warn] //> using")) == 2)
+        expect(runErrOut.contains("[warn] //> using options -Werror"))
+        // TODO: Warning about using directives in multiple files for the test scope should not be displayed
+        expect(runErrOut.contains("[warn] //> using scala \"3.2.2\""))
+      }
+
+      assertNoDiff(
+        os.read(includeRoot / "Included.scala"),
+        """//> using options -Werror
+          |
+          |case class Included(x: Int)
+          |""".stripMargin
+      )
+    }
+  }
+}
diff --git a/modules/options/src/main/scala/scala/build/options/SuppressWarningOptions.scala b/modules/options/src/main/scala/scala/build/options/SuppressWarningOptions.scala
index dc7cba7690..7846debcf3 100644
--- a/modules/options/src/main/scala/scala/build/options/SuppressWarningOptions.scala
+++ b/modules/options/src/main/scala/scala/build/options/SuppressWarningOptions.scala
@@ -9,4 +9,10 @@ final case class SuppressWarningOptions(
 object SuppressWarningOptions {
   implicit val hasHashData: HasHashData[SuppressWarningOptions] = HasHashData.derive
   implicit val monoid: ConfigMonoid[SuppressWarningOptions]     = ConfigMonoid.derive
+
+  val suppressAll = SuppressWarningOptions(
+    suppressDirectivesInMultipleFilesWarning = Some(true),
+    suppressOutdatedDependencyWarning = Some(true),
+    suppressExperimentalFeatureWarning = Some(true)
+  )
 }
diff --git a/website/docs/reference/cli-options.md b/website/docs/reference/cli-options.md
index 44927081dd..196819983e 100644
--- a/website/docs/reference/cli-options.md
+++ b/website/docs/reference/cli-options.md
@@ -56,7 +56,7 @@ Set JMH version
 
 Available in commands:
 
-[`bloop`](./commands.md#bloop), [`bloop exit`](./commands.md#bloop-exit), [`bloop output`](./commands.md#bloop-output), [`bloop start`](./commands.md#bloop-start), [`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test), [`uninstall`](./commands.md#uninstall)
+[`bloop`](./commands.md#bloop), [`bloop exit`](./commands.md#bloop-exit), [`bloop output`](./commands.md#bloop-output), [`bloop start`](./commands.md#bloop-start), [`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test), [`uninstall`](./commands.md#uninstall)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -229,7 +229,7 @@ Run given command against all provided Scala versions and/or platforms
 
 Available in commands:
 
-[`bloop`](./commands.md#bloop), [`bloop start`](./commands.md#bloop-start), [`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`config`](./commands.md#config), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`pgp push`](./commands.md#pgp-push), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
+[`bloop`](./commands.md#bloop), [`bloop start`](./commands.md#bloop-start), [`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`config`](./commands.md#config), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`pgp push`](./commands.md#pgp-push), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -249,7 +249,7 @@ Debug mode (attach by default)
 
 Available in commands:
 
-[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
+[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -424,7 +424,7 @@ Pass scalafmt version before running it (3.7.14 by default). If passed, this ove
 
 Available in commands:
 
-[`add-path`](./commands.md#add-path), [`bloop`](./commands.md#bloop), [`bloop exit`](./commands.md#bloop-exit), [`bloop output`](./commands.md#bloop-output), [`bloop start`](./commands.md#bloop-start), [`bsp`](./commands.md#bsp), [`clean`](./commands.md#clean), [`compile`](./commands.md#compile), [`config`](./commands.md#config), [`default-file`](./commands.md#default-file), [`dependency-update`](./commands.md#dependency-update), [`directories`](./commands.md#directories), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`help`](./commands.md#help), [`install completions` , `install-completions`](./commands.md#install-completions), [`install-home`](./commands.md#install-home), [`new`](./commands.md#new), [`package`](./commands.md#package), [`pgp pull`](./commands.md#pgp-pull), [`pgp push`](./commands.md#pgp-push), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`github secret create` , `gh secret create`](./commands.md#github-secret-create), [`github secret list` , `gh secret list`](./commands.md#github-secret-list), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test), [`uninstall`](./commands.md#uninstall), [`uninstall completions` , `uninstall-completions`](./commands.md#uninstall-completions), [`update`](./commands.md#update), [`version`](./commands.md#version)
+[`add-path`](./commands.md#add-path), [`bloop`](./commands.md#bloop), [`bloop exit`](./commands.md#bloop-exit), [`bloop output`](./commands.md#bloop-output), [`bloop start`](./commands.md#bloop-start), [`bsp`](./commands.md#bsp), [`clean`](./commands.md#clean), [`compile`](./commands.md#compile), [`config`](./commands.md#config), [`default-file`](./commands.md#default-file), [`dependency-update`](./commands.md#dependency-update), [`directories`](./commands.md#directories), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`help`](./commands.md#help), [`install completions` , `install-completions`](./commands.md#install-completions), [`install-home`](./commands.md#install-home), [`new`](./commands.md#new), [`package`](./commands.md#package), [`pgp pull`](./commands.md#pgp-pull), [`pgp push`](./commands.md#pgp-push), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`github secret create` , `gh secret create`](./commands.md#github-secret-create), [`github secret list` , `gh secret list`](./commands.md#github-secret-list), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test), [`uninstall`](./commands.md#uninstall), [`uninstall completions` , `uninstall-completions`](./commands.md#uninstall-completions), [`update`](./commands.md#update), [`version`](./commands.md#version)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -438,7 +438,7 @@ Suppress warnings about using experimental features
 
 Available in commands:
 
-[`add-path`](./commands.md#add-path), [`bloop`](./commands.md#bloop), [`bloop exit`](./commands.md#bloop-exit), [`bloop output`](./commands.md#bloop-output), [`bloop start`](./commands.md#bloop-start), [`bsp`](./commands.md#bsp), [`clean`](./commands.md#clean), [`compile`](./commands.md#compile), [`config`](./commands.md#config), [`default-file`](./commands.md#default-file), [`dependency-update`](./commands.md#dependency-update), [`directories`](./commands.md#directories), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`help`](./commands.md#help), [`install completions` , `install-completions`](./commands.md#install-completions), [`install-home`](./commands.md#install-home), [`new`](./commands.md#new), [`package`](./commands.md#package), [`pgp create`](./commands.md#pgp-create), [`pgp key-id`](./commands.md#pgp-key-id), [`pgp pull`](./commands.md#pgp-pull), [`pgp push`](./commands.md#pgp-push), [`pgp sign`](./commands.md#pgp-sign), [`pgp verify`](./commands.md#pgp-verify), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`github secret create` , `gh secret create`](./commands.md#github-secret-create), [`github secret list` , `gh secret list`](./commands.md#github-secret-list), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test), [`uninstall`](./commands.md#uninstall), [`uninstall completions` , `uninstall-completions`](./commands.md#uninstall-completions), [`update`](./commands.md#update), [`version`](./commands.md#version)
+[`add-path`](./commands.md#add-path), [`bloop`](./commands.md#bloop), [`bloop exit`](./commands.md#bloop-exit), [`bloop output`](./commands.md#bloop-output), [`bloop start`](./commands.md#bloop-start), [`bsp`](./commands.md#bsp), [`clean`](./commands.md#clean), [`compile`](./commands.md#compile), [`config`](./commands.md#config), [`default-file`](./commands.md#default-file), [`dependency-update`](./commands.md#dependency-update), [`directories`](./commands.md#directories), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`help`](./commands.md#help), [`install completions` , `install-completions`](./commands.md#install-completions), [`install-home`](./commands.md#install-home), [`new`](./commands.md#new), [`package`](./commands.md#package), [`pgp create`](./commands.md#pgp-create), [`pgp key-id`](./commands.md#pgp-key-id), [`pgp pull`](./commands.md#pgp-pull), [`pgp push`](./commands.md#pgp-push), [`pgp sign`](./commands.md#pgp-sign), [`pgp verify`](./commands.md#pgp-verify), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`github secret create` , `gh secret create`](./commands.md#github-secret-create), [`github secret list` , `gh secret list`](./commands.md#github-secret-list), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test), [`uninstall`](./commands.md#uninstall), [`uninstall completions` , `uninstall-completions`](./commands.md#uninstall-completions), [`update`](./commands.md#update), [`version`](./commands.md#version)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -462,7 +462,7 @@ Print help message, including hidden options, and exit
 
 Available in commands:
 
-[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
+[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -562,7 +562,7 @@ Add java properties. Note that options equal `-Dproperty=value` are assumed to b
 
 Available in commands:
 
-[`bloop`](./commands.md#bloop), [`bloop start`](./commands.md#bloop-start), [`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`config`](./commands.md#config), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`pgp push`](./commands.md#pgp-push), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
+[`bloop`](./commands.md#bloop), [`bloop start`](./commands.md#bloop-start), [`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`config`](./commands.md#config), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`pgp push`](./commands.md#pgp-push), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -612,7 +612,7 @@ Port for BSP debugging
 
 Available in commands:
 
-[`add-path`](./commands.md#add-path), [`bloop`](./commands.md#bloop), [`bloop exit`](./commands.md#bloop-exit), [`bloop output`](./commands.md#bloop-output), [`bloop start`](./commands.md#bloop-start), [`bsp`](./commands.md#bsp), [`clean`](./commands.md#clean), [`compile`](./commands.md#compile), [`config`](./commands.md#config), [`default-file`](./commands.md#default-file), [`dependency-update`](./commands.md#dependency-update), [`directories`](./commands.md#directories), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`help`](./commands.md#help), [`install completions` , `install-completions`](./commands.md#install-completions), [`install-home`](./commands.md#install-home), [`new`](./commands.md#new), [`package`](./commands.md#package), [`pgp pull`](./commands.md#pgp-pull), [`pgp push`](./commands.md#pgp-push), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`github secret create` , `gh secret create`](./commands.md#github-secret-create), [`github secret list` , `gh secret list`](./commands.md#github-secret-list), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test), [`uninstall`](./commands.md#uninstall), [`uninstall completions` , `uninstall-completions`](./commands.md#uninstall-completions), [`update`](./commands.md#update), [`version`](./commands.md#version)
+[`add-path`](./commands.md#add-path), [`bloop`](./commands.md#bloop), [`bloop exit`](./commands.md#bloop-exit), [`bloop output`](./commands.md#bloop-output), [`bloop start`](./commands.md#bloop-start), [`bsp`](./commands.md#bsp), [`clean`](./commands.md#clean), [`compile`](./commands.md#compile), [`config`](./commands.md#config), [`default-file`](./commands.md#default-file), [`dependency-update`](./commands.md#dependency-update), [`directories`](./commands.md#directories), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`help`](./commands.md#help), [`install completions` , `install-completions`](./commands.md#install-completions), [`install-home`](./commands.md#install-home), [`new`](./commands.md#new), [`package`](./commands.md#package), [`pgp pull`](./commands.md#pgp-pull), [`pgp push`](./commands.md#pgp-push), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`github secret create` , `gh secret create`](./commands.md#github-secret-create), [`github secret list` , `gh secret list`](./commands.md#github-secret-list), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test), [`uninstall`](./commands.md#uninstall), [`uninstall completions` , `uninstall-completions`](./commands.md#uninstall-completions), [`update`](./commands.md#update), [`version`](./commands.md#version)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -650,7 +650,7 @@ List main classes available in the current context
 
 Available in commands:
 
-[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
+[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -1099,7 +1099,7 @@ Dummy mode - don't upload any secret to GitHub
 
 Available in commands:
 
-[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
+[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -1202,7 +1202,7 @@ Run Java commands using a manifest-based class path (shortens command length)
 
 Available in commands:
 
-[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
+[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -1288,7 +1288,7 @@ Whether to run the Scala.js CLI on the JVM or using a native executable
 
 Available in commands:
 
-[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
+[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -1346,7 +1346,7 @@ Embed resources into the Scala Native binary (can be read with the Java resource
 
 Available in commands:
 
-[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
+[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -1360,7 +1360,7 @@ Add a `scalac` option. Note that options starting with `-g`, `-language`, `-opt`
 
 Available in commands:
 
-[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
+[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -1413,7 +1413,7 @@ Aliases: `-n`
 
 Available in commands:
 
-[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
+[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -1514,7 +1514,7 @@ Force object wrapper for scripts
 
 Available in commands:
 
-[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
+[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -1563,7 +1563,7 @@ A synonym to --markdown-snippet, which defaults the sub-command to `run` when no
 
 Available in commands:
 
-[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
+[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -1577,7 +1577,7 @@ Generate BuildInfo for project
 
 Available in commands:
 
-[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
+[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -1698,7 +1698,7 @@ A github token used to access GitHub. Not needed in most cases.
 
 Available in commands:
 
-[`add-path`](./commands.md#add-path), [`bloop`](./commands.md#bloop), [`bloop exit`](./commands.md#bloop-exit), [`bloop output`](./commands.md#bloop-output), [`bloop start`](./commands.md#bloop-start), [`bsp`](./commands.md#bsp), [`clean`](./commands.md#clean), [`compile`](./commands.md#compile), [`config`](./commands.md#config), [`default-file`](./commands.md#default-file), [`dependency-update`](./commands.md#dependency-update), [`directories`](./commands.md#directories), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`help`](./commands.md#help), [`install completions` , `install-completions`](./commands.md#install-completions), [`install-home`](./commands.md#install-home), [`new`](./commands.md#new), [`package`](./commands.md#package), [`pgp pull`](./commands.md#pgp-pull), [`pgp push`](./commands.md#pgp-push), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`github secret create` , `gh secret create`](./commands.md#github-secret-create), [`github secret list` , `gh secret list`](./commands.md#github-secret-list), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test), [`uninstall`](./commands.md#uninstall), [`uninstall completions` , `uninstall-completions`](./commands.md#uninstall-completions), [`update`](./commands.md#update), [`version`](./commands.md#version)
+[`add-path`](./commands.md#add-path), [`bloop`](./commands.md#bloop), [`bloop exit`](./commands.md#bloop-exit), [`bloop output`](./commands.md#bloop-output), [`bloop start`](./commands.md#bloop-start), [`bsp`](./commands.md#bsp), [`clean`](./commands.md#clean), [`compile`](./commands.md#compile), [`config`](./commands.md#config), [`default-file`](./commands.md#default-file), [`dependency-update`](./commands.md#dependency-update), [`directories`](./commands.md#directories), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`help`](./commands.md#help), [`install completions` , `install-completions`](./commands.md#install-completions), [`install-home`](./commands.md#install-home), [`new`](./commands.md#new), [`package`](./commands.md#package), [`pgp pull`](./commands.md#pgp-pull), [`pgp push`](./commands.md#pgp-push), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`github secret create` , `gh secret create`](./commands.md#github-secret-create), [`github secret list` , `gh secret list`](./commands.md#github-secret-list), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test), [`uninstall`](./commands.md#uninstall), [`uninstall completions` , `uninstall-completions`](./commands.md#uninstall-completions), [`update`](./commands.md#update), [`version`](./commands.md#version)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -1722,7 +1722,7 @@ Enable actionable diagnostics
 
 Available in commands:
 
-[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test), [`version`](./commands.md#version)
+[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test), [`version`](./commands.md#version)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -1852,7 +1852,7 @@ Name of BSP
 
 Available in commands:
 
-[`bloop`](./commands.md#bloop), [`bloop exit`](./commands.md#bloop-exit), [`bloop start`](./commands.md#bloop-start), [`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`config`](./commands.md#config), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`pgp push`](./commands.md#pgp-push), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`github secret create` , `gh secret create`](./commands.md#github-secret-create), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test), [`uninstall`](./commands.md#uninstall)
+[`bloop`](./commands.md#bloop), [`bloop exit`](./commands.md#bloop-exit), [`bloop start`](./commands.md#bloop-start), [`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`config`](./commands.md#config), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`pgp push`](./commands.md#pgp-push), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`github secret create` , `gh secret create`](./commands.md#github-secret-create), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test), [`uninstall`](./commands.md#uninstall)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -1905,7 +1905,7 @@ Force overwriting destination files
 
 Available in commands:
 
-[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
+[`bsp`](./commands.md#bsp), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
@@ -2107,7 +2107,7 @@ Available in commands:
 
 Available in commands:
 
-[`bsp`](./commands.md#bsp), [`clean`](./commands.md#clean), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
+[`bsp`](./commands.md#bsp), [`clean`](./commands.md#clean), [`compile`](./commands.md#compile), [`dependency-update`](./commands.md#dependency-update), [`doc`](./commands.md#doc), [`export`](./commands.md#export), [`fix`](./commands.md#fix), [`fmt` , `format` , `scalafmt`](./commands.md#fmt), [`package`](./commands.md#package), [`publish`](./commands.md#publish), [`publish local`](./commands.md#publish-local), [`publish setup`](./commands.md#publish-setup), [`repl` , `console`](./commands.md#repl), [`run`](./commands.md#run), [`setup-ide`](./commands.md#setup-ide), [`shebang`](./commands.md#shebang), [`test`](./commands.md#test)
 
 <!-- Automatically generated, DO NOT EDIT MANUALLY -->
 
diff --git a/website/docs/reference/commands.md b/website/docs/reference/commands.md
index aa2eac6151..4ea9c14c83 100644
--- a/website/docs/reference/commands.md
+++ b/website/docs/reference/commands.md
@@ -117,6 +117,28 @@ If you encounter any bugs or have feedback to share, make sure to reach out to t
 
 Accepts option groups: [compilation server](./cli-options.md#compilation-server-options), [coursier](./cli-options.md#coursier-options), [debug](./cli-options.md#debug-options), [dependency](./cli-options.md#dependency-options), [export](./cli-options.md#export-options), [global suppress warning](./cli-options.md#global-suppress-warning-options), [help group](./cli-options.md#help-group-options), [input](./cli-options.md#input-options), [jvm](./cli-options.md#jvm-options), [logging](./cli-options.md#logging-options), [main class](./cli-options.md#main-class-options), [markdown](./cli-options.md#markdown-options), [python](./cli-options.md#python-options), [Scala.js](./cli-options.md#scalajs-options), [Scala Native](./cli-options.md#scala-native-options), [scalac](./cli-options.md#scalac-options), [scalac extra](./cli-options.md#scalac-extra-options), [shared](./cli-options.md#shared-options), [snippet](./cli-options.md#snippet-options), [source generator](./cli-options.md#source-generator-options), [suppress warning](./cli-options.md#suppress-warning-options), [verbosity](./cli-options.md#verbosity-options), [version](./cli-options.md#version-options), [workspace](./cli-options.md#workspace-options)
 
+## fix
+
+Perform fixes on a Scala CLI project.
+
+Specific fix configurations can be specified with both command line options and using directives defined in sources.
+Command line options always take priority over using directives when a clash occurs, allowing to override configurations defined in sources.
+Using directives can be defined in all supported input source file types.
+
+Multiple inputs can be passed at once.
+Paths to directories, URLs and supported file types are accepted as inputs.
+Accepted file extensions: .scala, .sc, .java, .jar, .md, .jar, .c, .h, .zip
+For piped inputs use the corresponding alias: _.scala, _.java, _.sc, _.md
+All supported types of inputs can be mixed with each other.
+
+For detailed documentation refer to our website: https://scala-cli.virtuslab.org/docs/commands/fix
+
+The `fix` sub-command is experimental.
+Please bear in mind that non-ideal user experience should be expected.
+If you encounter any bugs or have feedback to share, make sure to reach out to the maintenance team at https://github.com/VirtusLab/scala-cli
+
+Accepts option groups: [compilation server](./cli-options.md#compilation-server-options), [coursier](./cli-options.md#coursier-options), [debug](./cli-options.md#debug-options), [dependency](./cli-options.md#dependency-options), [global suppress warning](./cli-options.md#global-suppress-warning-options), [help group](./cli-options.md#help-group-options), [input](./cli-options.md#input-options), [jvm](./cli-options.md#jvm-options), [logging](./cli-options.md#logging-options), [markdown](./cli-options.md#markdown-options), [python](./cli-options.md#python-options), [Scala.js](./cli-options.md#scalajs-options), [Scala Native](./cli-options.md#scala-native-options), [scalac](./cli-options.md#scalac-options), [scalac extra](./cli-options.md#scalac-extra-options), [shared](./cli-options.md#shared-options), [snippet](./cli-options.md#snippet-options), [source generator](./cli-options.md#source-generator-options), [suppress warning](./cli-options.md#suppress-warning-options), [verbosity](./cli-options.md#verbosity-options), [version](./cli-options.md#version-options), [workspace](./cli-options.md#workspace-options)
+
 ## fmt
 
 Aliases: `format`, `scalafmt`