Small fixes to make Metals work on large Pants workspaces

While testing the new Pants integration in a large Pants workspace I
encountered several issues related file watching and reading `*.jar`
files that have invalid ZIP byte contents.

metals/src/main/scala/scala/meta/internal/metals/FileWatcher.scala

@@ -10,6 +10,7 @@ import java.util.concurrent.CompletableFuture
 import java.util.concurrent.Executors
 import scala.meta.internal.metals.MetalsEnrichments._
 import scala.meta.io.AbsolutePath
+import java.{util => ju}
 
 /**
  * Handles file watching of interesting files in this build.
@@ -62,7 +63,7 @@ final class FileWatcher(
   }
 
   def restart(): Unit = {
-    val sourceDirectoriesToWatch = new util.ArrayList[Path]()
+    val sourceDirectoriesToWatch = new util.LinkedHashSet[Path]()
     val sourceFilesToWatch = new util.ArrayList[Path]()
     val createdSourceDirectories = new util.ArrayList[AbsolutePath]()
     def watch(path: AbsolutePath, isSource: Boolean): Unit = {
@@ -78,8 +79,11 @@ final class FileWatcher(
         // work on some other systems like Linux
         if (isSource) createdSourceDirectories.add(pathToCreate)
       }
-      if (path.isScalaOrJava) sourceFilesToWatch.add(path.toNIO)
-      else sourceDirectoriesToWatch.add(path.toNIO)
+      if (path.isScalaOrJava) {
+        sourceDirectoriesToWatch.add(path.toNIO.getParent())
+      } else {
+        sourceDirectoriesToWatch.add(path.toNIO)
+      }
     }
     // Watch the source directories for "goto definition" index.
     buildTargets.sourceItems.foreach(watch(_, isSource = true))
@@ -93,30 +97,20 @@ final class FileWatcher(
         )
       }
     }
-    startWatching(sourceFilesToWatch, sourceDirectoriesToWatch)
+    startWatching(new ju.ArrayList(sourceDirectoriesToWatch))
     createdSourceDirectories.asScala.foreach(_.delete())
   }
 
-  private def startWatching(
-      files: util.List[Path],
-      directories: util.List[Path]
-  ): Unit = {
+  private def startWatching(directories: util.List[Path]): Unit = {
     stopWatching()
     val directoryWatcher = DirectoryWatcher
       .builder()
       .paths(directories)
       .listener(new DirectoryListener())
+      .fileHashing(false)
       .build()
     activeDirectoryWatcher = Some(directoryWatcher)
     directoryWatching = directoryWatcher.watchAsync(directoryExecutor)
-
-    val fileWatcher = DirectoryWatcher
-      .builder()
-      .paths(files.map(_.getParent()))
-      .listener(new FileListener(watched = files.asScala.toSet))
-      .build()
-    activeFileWatcher = Some(fileWatcher)
-    fileWatching = fileWatcher.watchAsync(fileExecutor)
   }
 
   private def stopWatching(): Unit = {

metals/src/main/scala/scala/meta/internal/metals/JarTopLevels.scala

@@ -3,7 +3,6 @@ package scala.meta.internal.metals
 import java.nio.file.Files
 import java.nio.file.attribute.BasicFileAttributeView
 import java.sql.{Connection, PreparedStatement, Statement}
-
 import scala.collection.concurrent.TrieMap
 import scala.meta.internal.io.PlatformFileIO
 import scala.meta.internal.metals.JdbcEnrichments._

metals/src/main/scala/scala/meta/internal/metals/MetalsEnrichments.scala

@@ -34,6 +34,8 @@ import scala.meta.tokens.Token
 import scala.util.Properties
 import scala.{meta => m}
 import java.nio.file.StandardOpenOption
+import java.io.RandomAccessFile
+import scala.util.control.NonFatal
 
 /**
  * One stop shop for all extension methods that are used in the metals build.
@@ -270,6 +272,39 @@ object MetalsEnrichments
       FileIO.slurp(path, StandardCharsets.UTF_8)
     }
 
+    def isValidClasspathEntry(): Boolean =
+      path.isDirectory || hasZipMagicNumbers()
+
+    /**
+     * Returns true if this file can be read as a ZIP/Jar file.
+     *
+     * It's not sufficient to check the filename extension because `*.jar`
+     * files can contain non-ZIP contents causing `java.util.zip.ZipError`
+     * which is difficult to recover from.
+     */
+    def hasZipMagicNumbers(): Boolean = {
+      path.isFile && {
+        try {
+          val raf = new RandomAccessFile(path.toFile, "r")
+          try {
+            val n = raf.readInt()
+            n match {
+              // Magic numbers from https://en.wikipedia.org/wiki/List_of_file_signatures
+              case 0x504B0304 | 0x504B0506 | 0x504B0708 =>
+                true
+              case _ =>
+                false
+            }
+          } finally {
+            raf.close()
+          }
+        } catch {
+          case NonFatal(_) =>
+            false
+        }
+      }
+    }
+
     def isJar: Boolean = {
       val filename = path.toNIO.getFileName.toString
       filename.endsWith(".jar")

metals/src/main/scala/scala/meta/internal/metals/MetalsLanguageServer.scala

@@ -48,6 +48,7 @@ import scala.util.control.NonFatal
 import scala.util.Success
 import com.google.gson.JsonPrimitive
 import com.google.gson.JsonObject
+import java.util.zip.ZipError
 
 class MetalsLanguageServer(
     ec: ExecutionContextExecutorService,
@@ -1308,10 +1309,10 @@ class MetalsLanguageServer(
     }
     for {
       i <- statusBar.trackFuture("Importing build", importedBuild)
-      _ <- profiledIndexWorkspace { () =>
-        indexWorkspace(i)
-      }
-      _ = indexingPromise.trySuccess(())
+      _ <- profiledIndexWorkspace(
+        () => indexWorkspace(i),
+        () => indexingPromise.trySuccess(())
+      )
       _ <- Future.sequence[Unit, List](
         compilations
           .cascadeCompileFiles(buffers.open.toSeq)
@@ -1412,18 +1413,21 @@ class MetalsLanguageServer(
   }
 
   def profiledIndexWorkspace(
-      thunk: () => Unit
+      thunk: () => Unit,
+      onFinally: () => Unit
   ): Future[Unit] = {
     val tracked = statusBar.trackFuture(
       s"Indexing",
       Future {
         timedThunk("indexed workspace", onlyIf = true) {
           try thunk()
-          catch {
-            case NonFatal(e) =>
-              scribe.error("unexpected error indexing workspace", e)
+          finally {
+            onFinally()
           }
         }
+      }.recover {
+        case e: ZipError =>
+          scribe.error("unexpected error indexing workspace", e)
       }
     )
     tracked.foreach { _ =>
@@ -1521,9 +1525,10 @@ class MetalsLanguageServer(
     for {
       item <- dependencySources.getItems.asScala
       sourceUri <- Option(item.getSources).toList.flatMap(_.asScala)
+      path = sourceUri.toAbsolutePath
+      if path.isValidClasspathEntry()
     } {
       try {
-        val path = sourceUri.toAbsolutePath
         buildTargets.addDependencySource(path, item.getTarget)
         if (path.isJar) {
           usedJars += path

metals/src/main/scala/scala/meta/internal/metals/StatusBar.scala

@@ -197,8 +197,8 @@ final class StatusBar(
       timer.elapsedSeconds > 10 ||
         firstShow.exists(_.elapsedSeconds > 5)
     def isStale: Boolean = this match {
-      case Message(_) => (firstShow.isDefined && !isRecent) || isOutdated
-      case Progress(_, job, _, _) => job.isCompleted
+      case _: Message => (firstShow.isDefined && !isRecent) || isOutdated
+      case p: Progress => p.job.isCompleted
     }
   }
   private case class Message(params: MetalsStatusParams) extends Item

metals/src/main/scala/scala/meta/internal/metals/WorkspaceSymbolProvider.scala

@@ -9,6 +9,7 @@ import org.eclipse.{lsp4j => l}
 import scala.collection.concurrent.TrieMap
 import scala.concurrent.ExecutionContext
 import scala.meta.internal.mtags.OnDemandSymbolIndex
+import scala.meta.internal.metals.MetalsEnrichments._
 import scala.meta.internal.semanticdb.SymbolInformation.Kind
 import scala.meta.io.AbsolutePath
 import scala.meta.pc.SymbolSearch
@@ -90,6 +91,7 @@ final class WorkspaceSymbolProvider(
     packages.visitBootClasspath()
     for {
       classpathEntry <- buildTargets.allWorkspaceJars
+      if classpathEntry.isValidClasspathEntry()
     } {
       packages.visit(classpathEntry)
     }