o Updated to stop suppressing exception's thrown when closing streams.

o Updated to correctly test for end of file conditions.
o Catching up with the following 'commons-io' bug fixes:
    https://issues.apache.org/jira/browse/IO-298
    https://issues.apache.org/jira/browse/IO-502

src/main/java/org/codehaus/plexus/util/FileUtils.java

@@ -389,10 +389,12 @@ public static String fileRead( File file, String encoding )
             }
             int count;
             char[] b = new char[512];
-            while ( ( count = reader.read( b ) ) > 0 )  // blocking read
+            while ( ( count = reader.read( b ) ) >= 0 )  // blocking read
             {
                 buf.append( b, 0, count );
             }
+            reader.close();
+            reader = null;
         }
         finally
         {
@@ -439,6 +441,8 @@ public static void fileAppend( String fileName, String encoding, String data )
             {
                 out.write( data.getBytes() );
             }
+            out.close();
+            out = null;
         }
         finally
         {
@@ -515,6 +519,8 @@ public static void fileWrite( File file, String encoding, String data )
                 writer = new OutputStreamWriter( out );
             }
             writer.write( data );
+            writer.close();
+            writer = null;
         }
         finally
         {
@@ -761,18 +767,23 @@ public static boolean contentEquals( final File file1, final File file2 )
 
         InputStream input1 = null;
         InputStream input2 = null;
+        boolean equals = false;
         try
         {
             input1 = new FileInputStream( file1 );
             input2 = new FileInputStream( file2 );
-            return IOUtil.contentEquals( input1, input2 );
-
+            equals = IOUtil.contentEquals( input1, input2 );
+            input1.close();
+            input1 = null;
+            input2.close();
+            input2 = null;
         }
         finally
         {
             IOUtil.close( input1 );
             IOUtil.close( input2 );
         }
+        return equals;
     }
 
     /**
@@ -813,11 +824,11 @@ public static File toFile( final URL url )
     public static URL[] toURLs( final File[] files )
         throws IOException
     {
-        final URL[] urls = new URL[files.length];
+        final URL[] urls = new URL[ files.length ];
 
         for ( int i = 0; i < urls.length; i++ )
         {
-            urls[i] = files[i].toURL();
+            urls[i] = files[i].toURI().toURL();
         }
 
         return urls;
@@ -1112,6 +1123,14 @@ private static void doCopyFile( File source, File destination )
                 count = size - pos > FILE_COPY_BUFFER_SIZE ? FILE_COPY_BUFFER_SIZE : size - pos;
                 pos += output.transferFrom( input, pos, count );
             }
+            output.close();
+            output = null;
+            fos.close();
+            fos = null;
+            input.close();
+            input = null;
+            fis.close();
+            fis = null;
         }
         finally
         {
@@ -1197,6 +1216,10 @@ public static void copyStreamToFile( final InputStreamFacade source, final File
             input = source.getInputStream();
             output = new FileOutputStream( destination );
             IOUtil.copy( input, output );
+            output.close();
+            output = null;
+            input.close();
+            input = null;
         }
         finally
         {
@@ -2332,6 +2355,10 @@ public static void copyFile( File from, File to, String encoding, FilterWrapper[
                 }
 
                 IOUtil.copy( reader, fileWriter );
+                fileWriter.close();
+                fileWriter = null;
+                fileReader.close();
+                fileReader = null;
             }
             finally
             {

src/main/java/org/codehaus/plexus/util/IOUtil.java

@@ -186,7 +186,7 @@ public static void copy( final InputStream input,
     {
         final byte[] buffer = new byte[bufferSize];
         int n = 0;
-        while ( -1 != ( n = input.read( buffer ) ) )
+        while ( 0 <= ( n = input.read( buffer ) ) )
         {
             output.write( buffer, 0, n );
         }
@@ -210,7 +210,7 @@ public static void copy( final Reader input, final Writer output, final int buff
     {
         final char[] buffer = new char[bufferSize];
         int n = 0;
-        while ( -1 != ( n = input.read( buffer ) ) )
+        while ( 0 <= ( n = input.read( buffer ) ) )
         {
             output.write( buffer, 0, n );
         }
@@ -699,7 +699,7 @@ public static boolean contentEquals( final InputStream input1,
         final InputStream bufferedInput2 = new BufferedInputStream( input2 );
 
         int ch = bufferedInput1.read();
-        while ( -1 != ch )
+        while ( 0 <= ch )
         {
             final int ch2 = bufferedInput2.read();
             if ( ch != ch2 )
@@ -710,7 +710,7 @@ public static boolean contentEquals( final InputStream input1,
         }
 
         final int ch2 = bufferedInput2.read();
-        if ( -1 != ch2 )
+        if ( 0 <= ch2 )
         {
             return false;
         }

src/test/java/org/codehaus/plexus/util/IOUtilTest.java

@@ -127,7 +127,7 @@ private void assertEqualContent( File f0, File f1 )
 
         try
         {
-            while ( -1 != n0 )
+            while ( 0 <= n0 )
             {
                 n0 = is0.read( buf0 );
                 n1 = is1.read( buf1 );