diff --git a/Sources/JavaStdlib/JavaIO/swift-java.config b/Sources/JavaStdlib/JavaIO/swift-java.config
index 7b40b2da..571e0216 100644
--- a/Sources/JavaStdlib/JavaIO/swift-java.config
+++ b/Sources/JavaStdlib/JavaIO/swift-java.config
@@ -10,10 +10,10 @@
     "java.lang.Readable" : "Readable",
     "java.io.Writer" : "Writer",
     "java.io.File" : "File",
+    "java.io.Closeable" : "Closeable",
     "java.nio.file.Path" : "Path",
     "java.io.FileDescriptor" : "FileDescriptor",
     "java.nio.charset.Charset" : "Charset",
-    "java.io.Closeable" : "Closeable",
     "java.io.Flushable" : "Flushable",
     "java.io.Flushable" : "ByteBuffer",
     "java.nio.file.WatchService" : "WatchService",
diff --git a/Sources/SwiftJavaTool/Commands/ConfigureCommand.swift b/Sources/SwiftJavaTool/Commands/ConfigureCommand.swift
index 837d5e2f..455cb962 100644
--- a/Sources/SwiftJavaTool/Commands/ConfigureCommand.swift
+++ b/Sources/SwiftJavaTool/Commands/ConfigureCommand.swift
@@ -104,11 +104,11 @@ extension SwiftJava.ConfigureCommand {
     log.logLevel = .init(rawValue: self.logLevel.rawValue)!
 
     log.info("Run: emit configuration...")
-    var (amendExistingConfig, configuration) = try getBaseConfigurationForWrite()
+    var (amendExistingConfig, config) = try getBaseConfigurationForWrite()
 
     if !self.commonOptions.filterInclude.isEmpty {
       log.debug("Generate Java->Swift type mappings. Active include filters: \(self.commonOptions.filterInclude)")
-    } else if let filters = configuration.filterInclude, !filters.isEmpty { 
+    } else if let filters = config.filterInclude, !filters.isEmpty { 
       // take the package filter from the configuration file
       self.commonOptions.filterInclude = filters
     } else {
@@ -124,7 +124,7 @@ extension SwiftJava.ConfigureCommand {
     if amendExistingConfig {
       log.info("Amend existing swift-java.config file...")
     }
-    configuration.classpath = classpathEntries.joined(separator: ":") // TODO: is this correct?
+    config.classpath = classpathEntries.joined(separator: ":") // TODO: is this correct?
 
     // Import types from all the classpath entries;
     // Note that we use the package level filtering, so users have some control over what gets imported.
@@ -139,7 +139,7 @@ extension SwiftJava.ConfigureCommand {
       if entry.hasSuffix(".jar") {
         let jarFile = try JarFile(entry, false, environment: environment)
         try addJavaToSwiftMappings(
-          to: &configuration,
+          to: &config,
           forJar: jarFile,
           environment: environment
         )
@@ -151,7 +151,7 @@ extension SwiftJava.ConfigureCommand {
     }
 
     // Encode the configuration.
-    let contents = try configuration.renderJSON()
+    let contents = try config.renderJSON()
 
     // Write the file.
     try writeContents(
diff --git a/Sources/SwiftJavaTool/Commands/WrapJavaCommand.swift b/Sources/SwiftJavaTool/Commands/WrapJavaCommand.swift
index 0af1e75b..0e70ad00 100644
--- a/Sources/SwiftJavaTool/Commands/WrapJavaCommand.swift
+++ b/Sources/SwiftJavaTool/Commands/WrapJavaCommand.swift
@@ -66,6 +66,7 @@ extension SwiftJava {
 extension SwiftJava.WrapJavaCommand {
 
   mutating func runSwiftJavaCommand(config: inout Configuration) async throws {
+    print("self.commonOptions.filterInclude = \(self.commonOptions.filterInclude)")
     configure(&config.filterInclude, append: self.commonOptions.filterInclude)
     configure(&config.filterExclude, append: self.commonOptions.filterExclude)
 
@@ -114,6 +115,7 @@ extension SwiftJava.WrapJavaCommand {
 }
 
 extension SwiftJava.WrapJavaCommand {
+  
   mutating func generateWrappers(
     config: Configuration,
     dependentConfigs: [(String, Configuration)],
@@ -148,21 +150,9 @@ extension SwiftJava.WrapJavaCommand {
     let classLoader = try! JavaClass<ClassLoader>(environment: environment)
       .getSystemClassLoader()!
     var javaClasses: [JavaClass<JavaObject>] = []
-    eachClass: for (javaClassName, _) in config.classes ?? [:] {
-
-      // If we have an inclusive filter, import only types from it
-      for include in config.filterInclude ?? [] {
-        guard javaClassName.starts(with: include) else {
-          log.info("Skip Java type: \(javaClassName) (does not match filter)")
-          continue
-        }
-      }
-      // If we have an exclude filter, check for it as well
-      for exclude in config.filterExclude ?? [] { 
-        if javaClassName.starts(with: exclude) {
-          log.info("Skip Java type: \(javaClassName) (does match exclude filter: \(exclude))")
-          continue eachClass
-        }
+    for (javaClassName, _) in config.classes ?? [:] {
+      guard shouldImportJavaClass(javaClassName, config: config) else {
+        continue
       }
 
       log.info("Wrapping java type: \(javaClassName)")
@@ -213,19 +203,8 @@ extension SwiftJava.WrapJavaCommand {
           return nil
         }
 
-        // If we have an inclusive filter, import only types from it
-        for include in config.filterInclude ?? [] {
-          guard javaClassName.starts(with: include) else {
-            log.info("Skip Java type: \(javaClassName) (does not match filter)")
-            return nil
-          }
-        }
-        // If we have an exclude filter, check for it as well
-        for exclude in config.filterExclude ?? [] { 
-          if javaClassName.starts(with: exclude) {
-            log.info("Skip Java type: \(javaClassName) (does match exclude filter: \(exclude))")
-            return nil
-          }
+        guard shouldImportJavaClass(javaClassName, config: config) else {
+          return nil
         }
 
         // If this class has been explicitly mentioned, we're done.
@@ -285,4 +264,24 @@ extension SwiftJava.WrapJavaCommand {
       )
     }
   }
+
+  private func shouldImportJavaClass(_ javaClassName: String, config: Configuration) -> Bool {
+    // If we have an inclusive filter, import only types from it
+    for include in config.filterInclude ?? [] {
+      guard javaClassName.starts(with: include) else {
+        log.info("Skip Java type: \(javaClassName) (does not match include filter: \(include))")
+        return false
+      }
+    }
+    // If we have an exclude filter, check for it as well
+    for exclude in config.filterExclude ?? [] {
+      if javaClassName.starts(with: exclude) {
+        log.info("Skip Java type: \(javaClassName) (does match exclude filter: \(exclude))")
+        return false
+      }
+    }
+
+    // The class matches import filters, if any, and was not excluded.
+    return true
+  }
 }
diff --git a/Sources/SwiftJavaTool/CommonOptions.swift b/Sources/SwiftJavaTool/CommonOptions.swift
index ebdfdbea..c313202b 100644
--- a/Sources/SwiftJavaTool/CommonOptions.swift
+++ b/Sources/SwiftJavaTool/CommonOptions.swift
@@ -38,7 +38,11 @@ extension HasCommonOptions {
   
   func configure<T>(_ setting: inout [T]?, append value: [T]?) {
     if let value {
-      setting?.append(contentsOf: value)
+      if setting == nil {
+        setting = value
+      } else {
+        setting?.append(contentsOf: value)
+      }
     }
   }