nobuild 0.2: markdown javadoc, use newer Java methods

Build.java

@@ -1,10 +1,14 @@
 import static nobuild.NoBuild.*;
 
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
 import java.util.ArrayDeque;
 import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
+import java.util.logging.Level;
 import java.util.stream.Collectors;
 
 public class Build {
@@ -57,8 +61,9 @@ public class Build {
         break;
 
       case "package":
+        clean();
         buildJtags(mainClass, sourcePaths, classPaths);
-        packageJar(Optional.ofNullable(arguments.poll()));
+        packageJar(Optional.ofNullable(arguments.poll()).orElse("Jtags.jar"));
         break;
 
       case "test":
@@ -85,15 +90,34 @@ public class Build {
     }
   }
 
-  static void packageJar(Optional<String> jarfile) {
+  static void clean() {
+    command("rm", "-rf", buildClassPath + "/xyz");
+  }
+
+  static void packageJar(String jarfile) {
+    File file = new File(jarfile);
+    file.delete();
+
     command(
-        "jar",
-        "cfe",
-        jarfile.orElse("Jtags.jar"),
-        "xyz.naofal.jtags.Jtags",
-        "-C",
-        buildClassPath,
-        ".");
+        "jar", "cfe", jarfile, "xyz.naofal.jtags.Jtags", "-C", buildClassPath, "xyz/naofal/jtags");
+
+    // Make jar file executable by hashbang
+    byte[] hashbang = "#!/usr/bin/env -S java -jar\n".getBytes();
+    int fileLength = (int) file.length();
+    int length = fileLength + hashbang.length;
+    byte[] bytes = new byte[length];
+    System.arraycopy(hashbang, 0, bytes, 0, hashbang.length);
+    try {
+      FileInputStream in = new FileInputStream(file);
+      in.read(bytes, hashbang.length, fileLength);
+      in.close();
+      FileOutputStream out = new FileOutputStream(file);
+      out.write(bytes);
+      out.close();
+    } catch (Exception ex) {
+      logger.log(Level.SEVERE, "Problem during file IO with " + jarfile, ex);
+    }
+    file.setExecutable(true);
   }
 
   static void runTests(String[] args) {

nobuild/NoBuild.java

@@ -1,8 +1,4 @@
-/*
- * NoBuild system
- *
- * @version 0.1
- * @since 1.8
+/* NoBuild system
  *
  * MIT License
  *
@@ -32,89 +28,110 @@ import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.io.OutputStream;
 import java.net.URI;
 import java.net.URL;
 import java.nio.file.FileSystems;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.PathMatcher;
-import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.Objects;
+import java.util.Optional;
 import java.util.logging.Handler;
 import java.util.logging.Level;
 import java.util.logging.LogRecord;
 import java.util.logging.Logger;
-import java.util.stream.Collectors;
 import java.util.stream.Stream;
 import javax.tools.JavaCompiler;
 import javax.tools.JavaFileObject;
 import javax.tools.StandardJavaFileManager;
 import javax.tools.ToolProvider;
 
-/**
- * NoBuild system
- *
- * <h2>Quick Guide</h2>
- *
- * A simple build script:
- *
- * <pre>
- * // Build.java
- * import static nobuild.Nobuild.*;
- *
- * public class Build {
- *   public static void main(String[] args) {
- *     rebuildSelf(Build.class, args);
- *     compileJava("Hello.java");
- *     runJava("Hello");
- *   }
- * }
- * </pre>
- *
- * Which can be run as follows:
- *
- * <pre>
- * $ javac -d build/ Build.java
- * $ java -cp build/ Build
- * </pre>
- *
- * Note that by using {@link NoBuild#rebuildSelf}, the build script {@code Build} will automatically
- * rebuild itself if {@code Build.java} is modified.
- *
- * @author Naofal Helal
- * @version 0.1
- * @since 1.8
- */
+/// # NoBuild system
+///
+/// ## Quick Guide
+///
+/// A simple build script:
+///
+/// ```java
+/// // Build.java
+/// import static nobuild.Nobuild.*;
+///
+/// public class Build {
+///   public static void main(String[] args) {
+///     rebuildSelf(Build.class, args);
+///     compileJava("Hello.java");
+///     runJava("Hello");
+///   }
+/// }
+/// ```
+///
+/// Which can be run as follows:
+///
+/// ```console
+/// $ javac -d build/ Build.java
+/// $ java -cp build/ Build
+/// ```
+///
+/// or:
+///
+/// ```console
+/// $ java -cp build/ Build.java
+/// ```
+///
+/// Note that by using [rebuildSelf][#rebuildSelf], the build script `Build` will automatically
+/// rebuild itself if `Build.java` is modified.
+///
+/// @author Naofal Helal
+/// @version 0.2
+/// @since 23
+////
 public class NoBuild {
   public static Logger logger = Logger.getLogger("logger");
   public static Handler loggingHandler = new NoBuildLogHandler();
   public static JavaCompiler compiler = ToolProvider.getSystemJavaCompiler();
 
-  public static Path javaHome = Paths.get(System.getProperty("java.home"));
+  public static Path javaHome = Path.of(System.getProperty("java.home"));
   public static String javaBin = javaHome.resolve("bin", "java").toString();
   public static String javacBin = javaHome.resolve("bin", "javac").toString();
 
-  /** The class path used by the java executable */
+  /// The class path used by the java executable.
   public static String javaClassPath = System.getProperty("java.class.path");
 
-  /**
-   * Path to the build script class file, or {@code null} if {@link #rebuildSelf} hasn't been
-   * called.
-   *
-   * <p>Will be used as the default output directory for compilation.
-   */
+  /// Path to the build script class file, or `null` if [rebuildSelf][#rebuildSelf] hasn't been
+  /// called.
+  ///
+  /// Will be used as the default output directory for compilation.
   public static String buildClassPath = null;
 
-  /** Returns the class path of the build script */
+  /// Returns the class path of the build script.
   public static String defaultBuildClassPath(Class<?> buildClass) {
-    URL buildClassUrl = buildClass.getResource(buildClass.getName() + ".class");
-    return Paths.get(buildClassUrl.getPath()).getParent().toString();
+    URL buildClassUrl = buildClass.getResource(buildClass.getSimpleName() + ".class");
+    return Optional.ofNullable(Path.of(buildClassUrl.getPath()).getParent())
+        .orElseGet(
+            () -> {
+              Path path = Path.of(".", "build");
+              boolean isPathInClasspath =
+                  Arrays.stream(javaClassPath.split(File.pathSeparator))
+                      .anyMatch(
+                          it -> {
+                            try {
+                              return Files.isSameFile(Path.of(it), path);
+                            } catch (IOException e) {
+                              return false;
+                            }
+                          });
+              if (!isPathInClasspath) {
+                logger.warning(
+                    "Using %s as default classpath. Make sure to include with -cp %1$s"
+                        .formatted(path));
+              }
+              return path;
+            })
+        .toString();
   }
 
   static {
@@ -154,7 +171,7 @@ public class NoBuild {
     @Override
     public void publish(LogRecord record) {
       if (record.getMessage() != null && !record.getMessage().isEmpty()) {
-        if (System.console().isTerminal()) {
+        if (Optional.ofNullable(System.console()).map(it -> it.isTerminal()).orElse(false)) {
           int color = colors.get(record.getLevel());
           System.err.printf(
               "\u001b[38;5;%dm[%s]\u001b[0m %s%n",
@@ -164,30 +181,26 @@ public class NoBuild {
         }
       }
       if (record.getThrown() != null) {
-        System.err.println(indent(record.getThrown().toString(), 4));
+        System.err.println(record.getThrown().toString().indent(4));
       }
     }
   }
 
-  /**
-   * Rebuilds the build script if necessary
-   *
-   * @param buildClass The main class of the build script
-   * @param args arguments from the main method
-   */
+  /// Rebuilds the build script if necessary.
+  ///
+  /// @param buildClass The main class of the build script
+  /// @param args arguments from the main method
   public static void rebuildSelf(Class<?> buildClass, String[] args) {
     rebuildSelf(buildClass, args, new String[0]);
   }
 
-  /**
-   * Rebuilds the build script if necessary
-   *
-   * @param buildClass The main class of the build script
-   * @param args Arguments from the main method
-   * @param additionalSources Additional sources to watch and compile
-   */
+  /// Rebuilds the build script if necessary.
+  ///
+  /// @param buildClass The main class of the build script
+  /// @param args Arguments from the main method
+  /// @param additionalSources Additional sources to watch and compile
   public static void rebuildSelf(Class<?> buildClass, String[] args, String... additionalSources) {
-    String buildSource = buildClass.getName() + ".java";
+    String buildSource = buildClass.getName().replaceAll("\\.", File.separator) + ".java";
     buildClassPath = defaultBuildClassPath(buildClass);
 
     String[] sourcePaths =
@@ -196,7 +209,7 @@ public class NoBuild {
 
     if (!classNeedsRebuild(buildClass.getName(), sourcePaths)) return;
 
-    logger.info(String.format("Recompiling %s...", buildSource));
+    logger.info("Recompiling %s...".formatted(buildSource));
 
     if (!compileJava(buildClassPath, sourcePaths)) {
       logger.severe("Compilation failed");
@@ -207,35 +220,29 @@ public class NoBuild {
     System.exit(status);
   }
 
-  /**
-   * Runs a Java class
-   *
-   * @param mainClass The fully qualified class name, e.g. {@code com.example.MyClass$MySubClass}
-   * @return Exit status code
-   */
+  /// Runs a Java class.
+  ///
+  /// @param mainClass The fully qualified class name, e.g. `com.example.MyClass$MySubClass`
+  /// @return Exit status code
   public static int runJava(String mainClass) {
     return runJava(mainClass, new String[0]);
   }
 
-  /**
-   * Runs a Java class
-   *
-   * @param mainClass The fully qualified class name, e.g. {@code com.example.MyClass$MySubClass}
-   * @param args Arguments to pass to the main method
-   * @return Exit status code
-   */
+  /// Runs a Java class.
+  ///
+  /// @param mainClass The fully qualified class name, e.g. `com.example.MyClass$MySubClass`
+  /// @param args Arguments to pass to the main method
+  /// @return Exit status code
   public static int runJava(String mainClass, String... args) {
     return runJava(new String[0], mainClass, args);
   }
 
-  /**
-   * Runs a Java class
-   *
-   * @param additionalClassPaths Additional class paths to pass to the compiler
-   * @param mainClass The fully qualified class name, e.g. {@code com.example.MyClass$MySubClass}
-   * @param args Arguments to pass to the main method
-   * @return Exit status code
-   */
+  /// Runs a Java class.
+  ///
+  /// @param additionalClassPaths Additional class paths to pass to the compiler
+  /// @param mainClass The fully qualified class name, e.g. `com.example.MyClass$MySubClass`
+  /// @param args Arguments to pass to the main method
+  /// @return Exit status code
   public static int runJava(String[] additionalClassPaths, String mainClass, String... args) {
     String pathSeparator = System.getProperty("path.separator");
 
@@ -252,15 +259,13 @@ public class NoBuild {
     return command(commandLineStream.toArray(String[]::new));
   }
 
-  /**
-   * Runs a Java class
-   *
-   * @param additionalClassPaths Additional class paths to pass to the compiler
-   * @param javaArguments Arguments to pass to the java binary
-   * @param mainClass The fully qualified class name, e.g. {@code com.example.MyClass$MySubClass}
-   * @param args Arguments to pass to the main method
-   * @return Exit status code
-   */
+  /// Runs a Java class.
+  ///
+  /// @param additionalClassPaths Additional class paths to pass to the compiler
+  /// @param javaArguments Arguments to pass to the java binary
+  /// @param mainClass The fully qualified class name, e.g. `com.example.MyClass$MySubClass`
+  /// @param args Arguments to pass to the main method
+  /// @return Exit status code
   public static int runJava(
       String[] additionalClassPaths, String[] javaArguments, String mainClass, String... args) {
     String pathSeparator = System.getProperty("path.separator");
@@ -282,38 +287,30 @@ public class NoBuild {
     return command(commandLineStream.toArray(String[]::new));
   }
 
-  /**
-   * Compiles java sources
-   *
-   * @return {@code true} if all the sources compiled successfully
-   */
+  /// Compiles java sources.
+  ///
+  /// @return `true` if all the sources compiled successfully
   public static boolean compileJava(String... sourcePaths) {
     return compileJava(new String[0], buildClassPath, sourcePaths);
   }
 
-  /**
-   * Compiles java sources
-   *
-   * @return {@code true} if all the sources compiled successfully
-   */
+  /// Compiles java sources.
+  ///
+  /// @return `true` if all the sources compiled successfully
   public static boolean compileJava(String[] additionalClassPaths, String... sourcePaths) {
     return compileJava(additionalClassPaths, buildClassPath, sourcePaths);
   }
 
-  /**
-   * Compiles java sources
-   *
-   * @return {@code true} if all the sources compiled successfully
-   */
+  /// Compiles java sources.
+  ///
+  /// @return `true` if all the sources compiled successfully
   public static boolean compileJava(String classOutputPath, String... sourcePaths) {
     return compileJava(new String[0], classOutputPath, sourcePaths);
   }
 
-  /**
-   * Compiles java sources
-   *
-   * @return {@code true} if all the sources compiled successfully
-   */
+  /// Compiles java sources.
+  ///
+  /// @return `true` if all the sources compiled successfully
   public static boolean compileJava(
       String[] additionalClassPaths, String classOutputPath, String... sourcePaths) {
     try (StandardJavaFileManager fileManager =
@@ -342,11 +339,9 @@ public class NoBuild {
     }
   }
 
-  /**
-   * Runs a shell command
-   *
-   * @return Exit status code
-   */
+  /// Runs a shell command.
+  ///
+  /// @return Exit status code
   public static int command(String... command) {
     try {
       return commandThrows(command);
@@ -356,12 +351,10 @@ public class NoBuild {
     }
   }
 
-  /**
-   * Runs a shell command. May throw an {@code IOException}
-   *
-   * @return Exit status code
-   * @throws Exception
-   */
+  /// Runs a shell command. May throw an `IOException`.
+  ///
+  /// @return Exit status code
+  /// @throws Exception
   public static int commandThrows(String... command) throws IOException {
     ProcessBuilder pb = new ProcessBuilder(command).inheritIO();
     Process process;
@@ -376,27 +369,24 @@ public class NoBuild {
     }
   }
 
-  /**
-   * Returns file paths that match a {@code globPattern}
-   *
-   * @see java.nio.file.FileSystem#getPathMatcher(String) getPathMatcher
-   */
+  /// Returns file paths that match a `globPattern`.
+  ///
+  /// @see java.nio.file.FileSystem#getPathMatcher(String) getPathMatcher
   public static String[] glob(String globPattern) {
-    Path cwd = Paths.get(".");
+    Path cwd = Path.of(".");
     PathMatcher pathMatcher =
         FileSystems.getDefault()
             .getPathMatcher(String.join("", "glob:", cwd.toString(), File.separator, globPattern));
-    try (@SuppressWarnings("unused")
-        Stream<Path> paths =
-            Files.find(
-                cwd, Integer.MAX_VALUE, (path, basicFileAttributes) -> pathMatcher.matches(path))) {
+    try (Stream<Path> paths =
+        Files.find(
+            cwd, Integer.MAX_VALUE, (path, basicFileAttributes) -> pathMatcher.matches(path))) {
       return paths.map(Path::toString).toArray(String[]::new);
     } catch (IOException e) {
       return new String[0];
     }
   }
 
-  /** Checks if the {@code targetPath} needs to be rebuilt from {@code sourcePaths} */
+  /// Checks if the `targetPath` needs to be rebuilt from `sourcePaths`.
   public static boolean needsRebuild(String targetPath, String... sourcePaths) {
     long targetLastModified = new File(targetPath).lastModified();
     return targetLastModified == 0
@@ -404,7 +394,7 @@ public class NoBuild {
             .anyMatch(sourcePath -> new File(sourcePath).lastModified() > targetLastModified);
   }
 
-  /** Checks if the {@code targetPath} needs to be rebuilt from {@code sourcePaths} */
+  /// Checks if the `targetPath` needs to be rebuilt from `sourcePaths`.
   public static boolean needsRebuild(Path targetPath, Path... sourcePaths) {
     long targetLastModified = targetPath.toFile().lastModified();
     return targetLastModified == 0
@@ -412,21 +402,17 @@ public class NoBuild {
             .anyMatch(sourcePath -> sourcePath.toFile().lastModified() > targetLastModified);
   }
 
-  /**
-   * Checks if the class {@code className} needs to be rebuilt from {@code sourcePaths}
-   *
-   * @param className The fully qualified class name
-   */
+  /// Checks if the class `className` needs to be rebuilt from `sourcePaths`.
+  ///
+  /// @param className The fully qualified class name
   public static boolean classNeedsRebuild(String className, String... sourcePaths) {
     return classNeedsRebuild(buildClassPath, className, sourcePaths);
   }
 
-  /**
-   * Checks if the class {@code className} needs to be rebuilt from {@code sourcePaths}
-   *
-   * @param classPath Path to look for the class in
-   * @param className The fully qualified class name
-   */
+  /// Checks if the class `className` needs to be rebuilt from `sourcePaths`.
+  ///
+  /// @param classPath Path to look for the class in
+  /// @param className The fully qualified class name
   public static boolean classNeedsRebuild(
       String classPath, String className, String... sourcePaths) {
     String targetClass =
@@ -435,50 +421,13 @@ public class NoBuild {
     return needsRebuild(targetClass, sourcePaths);
   }
 
-  /** Indents lines in {@code str} with {@code n} spaces */
-  public static String indent(String str, int n) {
-    if (str.isEmpty()) {
-      return "";
-    } else {
-      StringBuilder sb = new StringBuilder(n);
-      for (int i = 0; i < n; i++) {
-        sb.append(" ");
-      }
-      String spaces = sb.toString();
-      return Arrays.stream(str.split("\n"))
-          .map(line -> spaces + line)
-          .collect(Collectors.joining("\n", "", "\n"));
-    }
-  }
-
-  /** Transfers bytes from IO streams {@code in} to {@code out} */
-  public static long transferTo(InputStream in, OutputStream out) throws IOException {
-    Objects.requireNonNull(out, "out");
-    long transferred = 0L;
-    byte[] buffer = new byte[16384];
-
-    int read;
-    while ((read = in.read(buffer, 0, 16384)) >= 0) {
-      out.write(buffer, 0, read);
-      if (transferred < Long.MAX_VALUE) {
-        try {
-          transferred = Math.addExact(transferred, (long) read);
-        } catch (ArithmeticException ex) {
-          transferred = Long.MAX_VALUE;
-        }
-      }
-    }
-
-    return transferred;
-  }
-
-  /** Downloads file from {@code url} to {@code destination} */
+  /// Downloads file from `url` to `destination`.
   public static boolean downloadArtefact(String url, Path destination) {
     try {
       InputStream urlStream = URI.create(url).toURL().openStream();
 
       Files.createDirectories(destination.getParent());
-      transferTo(urlStream, new FileOutputStream(destination.toFile()));
+      urlStream.transferTo(new FileOutputStream(destination.toFile()));
 
       return true;
     } catch (IOException ex) {
@@ -487,13 +436,13 @@ public class NoBuild {
     }
   }
 
-  /** Downloads file from {@code url} to {@code destination} */
+  /// Downloads file from `url` to `destination`.
   public static boolean downloadArtefact(URL url, Path destination) {
     try {
       InputStream urlStream = url.openStream();
 
       Files.createDirectories(destination.getParent());
-      transferTo(urlStream, new FileOutputStream(destination.toFile()));
+      urlStream.transferTo(new FileOutputStream(destination.toFile()));
 
       return true;
     } catch (IOException ex) {
@@ -502,26 +451,22 @@ public class NoBuild {
     }
   }
 
-  /** Describes a Java dependency */
+  /// Describes a Java dependency.
   public static record Dependency(String group, String name, String version) {}
 
-  /** URL template for maven central dependencies */
+  /// URL template for maven central dependencies.
   public static String mavenCentral = "https://repo1.maven.org/maven2/%1$s/%2$s/%3$s/%2$s-%3$s.jar";
 
-  /**
-   * Downloads {@code dependencies} from {@code repository}
-   *
-   * @param repository URL template for a repository, template arguments are provided:
-   *     <ul>
-   *       <li>{@code %1$s}: group id, delimeted with slashes
-   *       <li>{@code %2$s}: artefact name
-   *       <li>{@code %3$s}: artefact version
-   *     </ul>
-   *     See {@link NoBuild#mavenCentral}
-   * @param destination Path to download artefacts to
-   * @param dependencies Dependencies to download
-   * @return {@code true} if all dependencies were downloaded successfully
-   */
+  /// Downloads `dependencies` from `repository`.
+  ///
+  /// @param repository URL template for a repository, template arguments are provided:
+  ///     - `%1$s`: group id, delimeted with slashes
+  ///     - `%2$s`: artefact name
+  ///     - `%3$s`: artefact version
+  ///     See [mavenCentral][NoBuild#mavenCentral]
+  /// @param destination Path to download artefacts to
+  /// @param dependencies Dependencies to download
+  /// @return `true` if all dependencies were downloaded successfully
   public static boolean downloadDependencies(
       String repository, Path destination, Dependency... dependencies) {
     boolean success = true;

src/main/java/xyz/naofal/jtags/ArchiveExtractor.java

@@ -0,0 +1,45 @@
+package xyz.naofal.jtags;
+
+import static xyz.naofal.jtags.JtagsLogger.logger;
+
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.regex.Pattern;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+public class ArchiveExtractor {
+  static List<String> extractArchive(Path archive, Path destination, String pattern) {
+    logger.info("Extracting " + archive.toString() + "...");
+    List<String> extractedPaths = new ArrayList<>();
+    Pattern compiledPattern = Pattern.compile(pattern);
+    try (InputStream in = new FileInputStream(archive.toFile());
+        ZipInputStream zis = new ZipInputStream(in); ) {
+      ZipEntry entry;
+      while ((entry = zis.getNextEntry()) != null) {
+        logger.finest("Extracting " + entry.getName() + "...");
+        if (!compiledPattern.matcher(entry.getName()).matches()) {
+          zis.closeEntry();
+          entry = zis.getNextEntry();
+          continue;
+        }
+        Path entryPath = destination.resolve(entry.getName());
+        Files.createDirectories(entryPath.getParent());
+        logger.finest(() -> "Extracting " + entryPath.toString() + "...");
+        var bytes = zis.readAllBytes();
+        Files.write(entryPath, bytes);
+        extractedPaths.add(entryPath.toString());
+        zis.closeEntry();
+      }
+      return extractedPaths;
+    } catch (IOException ex) {
+      logger.severe(ex.toString());
+      return List.of();
+    }
+  }
+}

src/main/java/xyz/naofal/jtags/Jtags.java

@@ -7,6 +7,7 @@ import java.util.ArrayDeque;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
+import java.util.Optional;
 
 public class Jtags {
   static class Options {
@@ -17,6 +18,7 @@ public class Jtags {
     boolean excludeAnonymous = false;
     List<Class<? extends TagField>> fields =
         List.of(TagField.StaticTag.class, TagField.Package.class, TagField.EnclosingType.class);
+    Optional<Path> extractPath = Optional.empty();
   }
 
   public static void main(String[] args) {
@@ -104,11 +106,26 @@ public class Jtags {
                   System.exit(1);
                   yield null;
                 }
-                case String output -> Path.of(output);
+                case "-" -> Path.of("-");
+                case String output -> Path.of(output).toAbsolutePath();
               };
           logger.config("Writing tags to " + options.output.toString());
           break;
 
+        case "-extract-dir":
+          options.extractPath =
+              switch (arguments.poll()) {
+                case null -> {
+                  logger.severe("Expected argument after " + argument);
+                  printUsage();
+                  System.exit(1);
+                  yield null;
+                }
+                case String dir -> Optional.of(Path.of(dir).toAbsolutePath());
+              };
+          logger.config("Extracting JARs to " + options.extractPath.toString());
+          break;
+
         default:
           options.sources.add(argument);
           break;
@@ -137,7 +154,7 @@ public class Jtags {
 Usage: jtags [options] <sources...>
 Options:
   -o, -output <file>  Write tags to specified <file>
-                      Use - for standard output
+                      Use - for standard output. Default: tags
   -lib                Treat sources as third-party libraries
                       (alias for -no-non-public -no-anonymous)
   -no-anonymous       Exclude anonymous classes
@@ -148,6 +165,7 @@ Options:
                         s  static tag
                         p  package
                         t  enclosing type
+  -extract-dir <dir>  Extract JAR and ZIP archives to <dir>
   -h, -help           Show this message
 """);
   }

src/main/java/xyz/naofal/jtags/JtagsLogger.java

@@ -2,6 +2,7 @@ package xyz.naofal.jtags;
 
 import java.util.HashMap;
 import java.util.Map;
+import java.util.Optional;
 import java.util.logging.Handler;
 import java.util.logging.Level;
 import java.util.logging.LogRecord;
@@ -47,7 +48,7 @@ public class JtagsLogger {
     @Override
     public void publish(LogRecord record) {
       if (record.getMessage() != null && !record.getMessage().isEmpty()) {
-        if (System.console().isTerminal()) {
+        if (Optional.ofNullable(System.console()).map(it->it.isTerminal()).orElse(false)) {
           int color = colors.get(record.getLevel());
           System.err.printf(
               "\u001b[38;5;%dm[%s]\u001b[0m %s%n",

src/main/java/xyz/naofal/jtags/TagCollector.java

@@ -5,11 +5,12 @@ import static xyz.naofal.jtags.JtagsLogger.logger;
 import com.sun.source.tree.CompilationUnitTree;
 import com.sun.source.util.JavacTask;
 import com.sun.source.util.Trees;
+import java.io.IOException;
+import java.nio.file.Path;
 import java.util.AbstractQueue;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.PriorityBlockingQueue;
-import java.util.concurrent.TimeUnit;
+import java.util.Arrays;
+import java.util.Objects;
+import java.util.stream.Stream;
 import javax.tools.JavaCompiler;
 import javax.tools.JavaFileObject;
 import javax.tools.StandardJavaFileManager;
@@ -23,31 +24,61 @@ public class TagCollector {
   public static AbstractQueue<Tag> collectTags(Options options) {
     try (StandardJavaFileManager fileManager = compiler.getStandardFileManager(null, null, null)) {
 
-      Iterable<? extends JavaFileObject> compilationUnits =
-          fileManager.getJavaFileObjects(options.sources.toArray(String[]::new));
+      String[] sources = resolveSources(options);
+      logger.finest(() -> "Collecting tags from sources: " + Arrays.toString(sources));
+
+      Iterable<? extends JavaFileObject> compilationUnits = fileManager.getJavaFileObjects(sources);
 
-      logger.info("Parsing sources...");
       JavacTask task =
           (JavacTask) compiler.getTask(null, fileManager, null, null, null, compilationUnits);
       Iterable<? extends CompilationUnitTree> trees = task.parse();
 
-      logger.info("Collecting tags...");
+      TreeVisitor treeVisitor = new TreeVisitor(options);
+      TreeVisitorContext context = new TreeVisitorContext(Trees.instance(task));
 
-      Trees treeUtils = Trees.instance(task);
-      AbstractQueue<Tag> tags = new PriorityBlockingQueue<>();
-
-      TreeVisitor treeVisitor = new TreeVisitor(options, tags);
       for (CompilationUnitTree compilationUnitTree : trees) {
-              TreeVisitorContext context = new TreeVisitorContext(compilationUnitTree, treeUtils);
-              treeVisitor.scan(compilationUnitTree, context);
+        treeVisitor.scan(compilationUnitTree, context);
       }
 
-      return tags;
+      return treeVisitor.tags;
 
-    } catch (Exception ex) {
+    } catch (IOException ex) {
       logger.severe(ex.toString());
       System.exit(1);
       return null;
     }
   }
+
+  static String[] resolveSources(Options options) {
+    return options.sources.stream()
+        .flatMap(
+            path ->
+                switch (path) {
+                  case String _ when path.endsWith(".java") -> Stream.of(path);
+                  case String _ when path.endsWith(".jar") || path.endsWith(".zip") -> {
+                    if (options.extractPath.isEmpty()) {
+                      logger.severe("Archive file specified, but no -extract-dir");
+                      System.exit(1);
+                    }
+                    Path archivePath = Path.of(path);
+                    String archiveName = archivePath.getFileName().toString();
+                    yield ArchiveExtractor.extractArchive(
+                        archivePath,
+                        options
+                            .extractPath
+                            .get()
+                            .resolve(archiveName.substring(0, archiveName.lastIndexOf('.'))),
+                        "^.*\\.java$")
+                        .stream();
+                  }
+                  default -> {
+                    logger.warning("Ignoring unsupported source: " + path);
+                    yield Stream.of();
+                  }
+                })
+        .filter(Objects::nonNull)
+        // TODO: support package-info and module-info
+        .filter(it -> !it.endsWith("package-info.java") && !it.endsWith("module-info.java"))
+        .toArray(String[]::new);
+  }
 }

src/main/java/xyz/naofal/jtags/TagsWriter.java

@@ -17,6 +17,7 @@ public record TagsWriter(Options options) {
   private static final int MAX_PATTERN_LENGTH = 96;
 
   public boolean writeTagsFile(AbstractQueue<Tag> tags) {
+    logger.fine("Writing tags to " + options().output.toString());
     try (var outputStream =
             options().output.toString().equals("-")
                 ? System.out

src/main/java/xyz/naofal/jtags/TreeVisitor.java

@@ -13,30 +13,39 @@ import java.util.AbstractQueue;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
+import java.util.concurrent.PriorityBlockingQueue;
 import javax.lang.model.element.Modifier;
 import xyz.naofal.jtags.Jtags.Options;
 
 public class TreeVisitor extends TreePathScanner<Void, TreeVisitorContext> {
   public final Options options;
-  public final AbstractQueue<Tag> tags;
+  public final AbstractQueue<Tag> tags = new PriorityBlockingQueue<>();
 
-  public TreeVisitor(Options options, AbstractQueue<Tag> tagQueue) {
+  public TreeVisitor(Options options) {
     this.options = options;
-    this.tags = tagQueue;
   }
 
   @Override
   public Void visitCompilationUnit(CompilationUnitTree node, TreeVisitorContext p) {
+    p.compilationUnitTree = node;
+
     logger.fine(() -> "Collecting tags in file: " + p.getLocation());
 
+    if (node.getPackage() != null) {
+      scan(node.getPackage(), p);
+    }
+
     return scan(node.getTypeDecls(), p);
   }
 
   @Override
   public Void visitPackage(PackageTree node, TreeVisitorContext p) {
     Tag tag =
-        new Tag(
-            TagKind.PACKAGE, node.getPackageName().toString(), p.getLocation(), p.getLine(node));
+        new Tag(TagKind.PACKAGE, node.getPackageName().toString(), p.getLocation().getParent(), "");
+
+    if (tags.contains(tag)) {
+      return null;
+    }
 
     logger.finer(() -> "Package: " + tag);
 

src/main/java/xyz/naofal/jtags/TreeVisitorContext.java

@@ -16,12 +16,11 @@ import java.util.Optional;
 public class TreeVisitorContext {
   final Trees trees;
   final SourcePositions sourcePositions;
-  final CompilationUnitTree compilationUnitTree;
+  public CompilationUnitTree compilationUnitTree;
 
-  public TreeVisitorContext(CompilationUnitTree compilationUnitTree, Trees trees) {
-    this.compilationUnitTree = compilationUnitTree;
+  public TreeVisitorContext(Trees trees) {
     this.trees = trees;
-    this.sourcePositions = trees.getSourcePositions();
+    sourcePositions = trees.getSourcePositions();
   }
 
   public Path getLocation() {
@@ -33,10 +32,12 @@ public class TreeVisitorContext {
     long offset = getOffsetInSource(compilationUnitTree, node);
     try (var reader = new BufferedReader(compilationUnitTree.getSourceFile().openReader(true))) {
       long skipped = 0;
+      String prevLine = "";
       while (true) {
         String line = reader.readLine();
-        if (line == null) throw new RuntimeException("Reached the end of the stream");
+        if (line == null) return prevLine;
         skipped += line.length() + 1;
+        prevLine = line;
         if (skipped >= offset) return line;
       }
     } catch (Exception e) {

src/test/java/TestJtags.java

@@ -1,13 +1,6 @@
 import static notest.Test.Util.*;
 
 import java.io.IOException;
-import java.io.InputStream;
-import java.net.URI;
-import java.net.URL;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipInputStream;
 import notest.Test;
 
 class TestJtags {
@@ -25,70 +18,10 @@ class TestJtags {
             Jtags,
             "-o",
             "-",
-            "src/test/resources/BasicExample.java");
+            "src/test/java/examples/BasicExample.java");
 
     var tags = readAllLines(process.inputReader());
 
     getSnapshot().assertEquals(tags);
   }
-
-  static void downloadOpenjdkSources() throws IOException {
-    Path destination = Path.of("src", "test", "resources", "downloads");
-    if (Files.exists(destination.resolve("openjdk-src"))) return;
-
-    URL openjdkSrcZipURL =
-        URI.create("https://github.com/openjdk/jdk24u/archive/refs/tags/jdk-24+36.zip").toURL();
-    Path openjdkSrcZip = destination.resolve("jdk-24+36.zip");
-
-    if (!Files.exists(openjdkSrcZip)) {
-      System.err.println("Downloading openjdk sources jdk-24+36.zip (~118MB)...");
-      openjdkSrcZipURL
-          .openConnection()
-          .getInputStream()
-          .transferTo(Files.newOutputStream(openjdkSrcZip));
-    }
-
-    System.err.println("Extracting openjdk sources...");
-
-    Files.createDirectories(destination.resolve("openjdk-src"));
-
-    try (InputStream in = Files.newInputStream(openjdkSrcZip);
-        ZipInputStream zin = new ZipInputStream(in)) {
-      ZipEntry entry;
-      while ((entry = zin.getNextEntry()) != null) {
-        if (!entry.getName().startsWith("jdk24u-jdk-24-36/src/j")) {
-          zin.closeEntry();
-          entry = zin.getNextEntry();
-          continue;
-        }
-        Path entryPath =
-            destination.resolve(
-                "openjdk-src", entry.getName().substring("jdk24u-jdk-24-36/src/".length()));
-        if (entry.isDirectory()) {
-          Files.createDirectories(entryPath);
-        } else {
-          var bytes = zin.readAllBytes();
-          Files.write(entryPath, bytes);
-        }
-        zin.closeEntry();
-      }
-    }
-  }
-
-  @Test
-  static void openjdkSources() throws IOException {
-    downloadOpenjdkSources();
-
-    // var process =
-    //     runJava(
-    //         new String[] {"-Dlogger.level=CONFIG"},
-    //         Jtags,
-    //         Stream.concat(Stream.of("-o", "-"),
-    // Arrays.stream(glob("src/test/resources/downloads/**/.java")))
-    //             .toArray(String[]::new));
-
-    // var tags = readAllLines(process.inputReader());
-
-    // getSnapshot().assertEquals(tags);
-  }
 }

src/test/java/notest/Test.java

@@ -76,8 +76,7 @@ public @interface Test {
         case "-u", "-update-snapshots":
           options.updateSnapshots = true;
           break;
-        case null:
-        default:
+        case null, default:
           break;
       }
 

src/test/java/snapshots/TestJtags.basicExample.1

@@ -1,9 +1,9 @@
+ABC
 !_TAG_FILE_ENCODING	utf-8
 !_TAG_FILE_SORTED	2	/0=unsorted, 1=sorted, 2=foldcase/
-BasicExample	src/test/resources/BasicExample.java	/^public class BasicExample {$/;"	Cls	package:examples
-InnerClass	src/test/resources/BasicExample.java	/^    class InnerClass {$/;"	Cls	package:examples	class:BasicExample
-method1	src/test/resources/BasicExample.java	/^  private boolean method1() {$/;"	mthd	class:BasicExample
-method2	src/test/resources/BasicExample.java	/^          void method2() {}$/;"	mthd	class:(Anonymous)
-method2	src/test/resources/BasicExample.java	/^  public static void method2($/;"	mthd	file:	class:BasicExample
-method3	src/test/resources/BasicExample.java	/^      void method3() {}$/;"	mthd	class:InnerClass
-method4	src/test/resources/BasicExample.java	/^      private void method4() {}$/;"	mthd	class:InnerClass
+InnerClass	src/test/java/examples/BasicExample.java	/^    class InnerClass {$/;"	Cls	package:examples	class:BasicExample
+method1	src/test/java/examples/BasicExample.java	/^  private boolean method1() {$/;"	mthd	class:BasicExample
+method2	src/test/java/examples/BasicExample.java	/^          void method2() {}$/;"	mthd	class:(Anonymous)
+methodX	src/test/java/examples/BasicExample.java	/^  public static void method2($/;"	mthd	file:	class:BasicExample
+method3	src/test/java/examples/BasicExample.java	/^      void method3() {}$/;"	mthd	class:InnerClass
+method4	src/test/java/examples/BasicExample.java	/^      private void method4() {}$/;"	mthd	class:InnerClass