In my Java code I use a FileVisitor to traverse a filesystem and creating a structure of Paths, then later on this is converted to a json object for rendering in html.
Running on Windows it runs okay even against a linux filesystem, running on Linux against the same (now local) filesystem it fails to render special characters properly when call toString() on a path
i.e Windows debug output
CreateFolderTree:createJsonData:SEVERE: AddingNode(1):Duarte Lôbo- Requiem
and html displays ok as
Duarte Lôbo- Requiem
but linux debug output gives
CreateFolderTree:createJsonData:SEVERE: AddingNode(1):Duarte L??bo- Requiem
and html displays as two black diamond with question mark in them instead of the ô char
Why is this happening, the Paths are provided by the the FileVisitor class so must be getting constructed properly (i.e I am not hacking it myself) , and then i just call toString() on the path.
Is it a fonts problem, I have had some issues with fonts on the linux system but here I am just returning Strings to the html so cannot see a conection.
Probably an encoding issue, but I cant see a place where I am explicitly setting an encoding
Bulk of code below, debugging showing invalid output for linux is in the createJsonData() method
Edit:I have fixed the logging issue so that the output is written as UTF-8
  FileHandler fe = new FileHandler(logFileName, LOG_SIZE_IN_BYTES, 10, true);
  fe.setEncoding(StandardCharsets.UTF_8.name());
So we now see Windows is outputting correctly
CreateFolderTree:createJsonData:SEVERE: AddingNode(1):Duarte Lôbo- Requiem
but Linux is outputting
CreateFolderTree:createJsonData:SEVERE: AddingNode(1):Duarte L��bo- Requiem
and if I view this in HexEditor it gives this output for L��bo
4C EF BF BD EF BF BD 62 6F
Edit:Partial Solution
I came across What exactly is sun.jnu.encoding?
and found it was recommended to add this
 -Dsun.jnu.encoding=UTF-8
and it worked files were now displayed okay
Unfortunately if user then clicked on such a file and sent back to server I now get this error
java.lang.NullPointerException
    at java.base/sun.nio.fs.UnixPath.normalizeAndCheck(Unknown Source)
    at java.base/sun.nio.fs.UnixPath.<init>(Unknown Source)
    at java.base/sun.nio.fs.UnixFileSystem.getPath(Unknown Source)
    at java.base/java.nio.file.Paths.get(Unknown Source)
    at com.jthink.songkong.server.callback.ServerFixSongs.configureFileMapping(ServerFixSongs.java:59)
    at com.jthink.songkong.server.callback.ServerFixSongs.startTask(ServerFixSongs.java:88)
    at com.jthink.songkong.server.CmdRemote.lambda$null$36(CmdRemote.java:107) 
I tried adding -Dfile.encoding=UTF-8 both in addtion or instead of the jnu option and that didnt help , the jnu option was the one I needed.
I shoudn't have to add this undocumented sun-jnu-encoding option so it seems to be that the server is broken in some way ?
Code
   import com.google.common.base.Strings;
    import com.google.gson.Gson;
    import com.google.gson.GsonBuilder;
    import com.jthink.songkong.analyse.analyser.Counters;
    import com.jthink.songkong.analyse.general.Errors;
    import com.jthink.songkong.cmdline.SongKong;
    import com.jthink.songkong.fileloader.RecycleBinFolderNames;
    import com.jthink.songkong.server.fs.Data;
    import com.jthink.songkong.server.fs.PathWalker2;
    import com.jthink.songkong.server.fs.State;
    import com.jthink.songkong.ui.MainWindow;
    import com.jthink.songkong.ui.progressdialog.FixSongsCounters;
    import spark.Request;
    import spark.Response;
    import java.io.IOException;
    import java.net.UnknownHostException;
    import java.nio.file.*;
    import java.nio.file.attribute.BasicFileAttributes;
    import java.util.ArrayList;
    import java.util.HashSet;
    import java.util.Map;
    import java.util.Set;
    import java.util.logging.Level;
    /**
     * Count the number of files that can be loaded, for information purposes only
     */
    public class CreateFolderTree
    {
        private Path treeRoot;
        Set<Path> keys = new HashSet<Path>();
        public static class VisitFolder
                extends SimpleFileVisitor<Path>
        {
            private Set<Path> keys;
            private Integer maxDepth;
            private int depth;
            public VisitFolder(Set<Path> keys, Integer maxDepth)
            {
                this.keys=keys;
                this.maxDepth = maxDepth;
            }
            /**
             *
             * @param dir
             * @param attrs
             * @return
             * @throws IOException
             */
             /*
             * Ignore some dirs
             * @param dir
             * @param attrs
             * @return
             * @throws IOException
             */
            public FileVisitResult preVisitDirectory(Path dir, BasicFileAttributes attrs)
                    throws IOException
            {
                try
                {
                    if (dir.toFile().getName().equals(".AppleDouble"))
                    {
                        return FileVisitResult.SKIP_SUBTREE;
                    }
                    else if (dir.toString().equals("/proc"))
                    {
                        return FileVisitResult.SKIP_SUBTREE;
                    }
                    else if (dir.toString().equals("/dev"))
                    {
                        return FileVisitResult.SKIP_SUBTREE;
                    }
                    else if (RecycleBinFolderNames.isMatch(dir.toFile().getName()))
                    {
                        MainWindow.logger.log(Level.SEVERE, "Ignoring " + dir.toString());
                        return FileVisitResult.SKIP_SUBTREE;
                    }
                    else if (dir.toString().toLowerCase().endsWith(".tar"))
                    {
                        return FileVisitResult.SKIP_SUBTREE;
                    }
                    depth++;
                    if(depth > maxDepth)
                    {
                        depth--;
                        return FileVisitResult.SKIP_SUBTREE;
                    }
                    keys.add(dir);
                    return super.preVisitDirectory(dir, attrs);
                }
                catch(IOException e)
                {
                    MainWindow.logger.warning("Unable visit dir:"+dir + ":"+e.getMessage());
                    return FileVisitResult.SKIP_SUBTREE;
                }
            }
            /**
             *
             * Tar check due to http://stackoverflow.com/questions/14436032/why-is-java-7-files-walkfiletree-throwing-exception-on-encountering-a-tar-file-o/14446993#14446993
             * SONGKONG-294:Ignore exceptions if file is not readable
             *
             * @param file
             * @param exc
             * @return
             * @throws IOException
             */
            @Override
            public FileVisitResult visitFileFailed(Path file, IOException exc) throws IOException
            {
                if (file.toString().endsWith(".tar")) {
                    //We dont log to reports as this is a bug in Java that we are handling not a problem in SongKong
                    MainWindow.logger.log(Level.SEVERE, exc.getMessage());
                    return FileVisitResult.CONTINUE;
                }
                try
                {
                    FileVisitResult result = super.visitFileFailed(file, exc);
                    return result;
                }
                catch(IOException e)
                {
                    MainWindow.logger.warning("Unable to visit file:"+file + ":"+e.getMessage());
                    return FileVisitResult.CONTINUE;
                }
            }
            /**
             * SONGKONG-294:Ignore exception if folder is not readable
             *
             * @param dir
             * @param exc
             * @return
             * @throws IOException
             */
            @Override
            public FileVisitResult postVisitDirectory(Path dir, IOException exc)
                    throws IOException
            {
                depth--;
                try
                {
                    FileVisitResult result = super.postVisitDirectory(dir, exc);
                    return result;
                }
                catch(IOException e)
                {
                    MainWindow.logger.warning("Unable to count files in dir(2):"+dir);
                    return FileVisitResult.CONTINUE;
                }
            }
        }
        public CreateFolderTree(Path treeRoot)
        {
            this.treeRoot = treeRoot;
        }
        public String start(int depth)
        {
            VisitFolder visitFolder;
            try
            {
                if(treeRoot==null)
                {
                    for (Path path : FileSystems.getDefault().getRootDirectories())
                    {
                        visitFolder = new VisitFolder(keys, depth);
                        Files.walkFileTree(path, visitFolder);
                    }
                }
                else
                {
                    visitFolder = new VisitFolder(keys, depth);
                    Files.walkFileTree(treeRoot, visitFolder);
                }
                PathWalker2 pw = new PathWalker2();
                for (Path key : keys)
                {
                    //SONGKONG-505: Illegal character in Filepath problem prevented reportFile creation
                    try
                    {
                        pw.addPath(key);
                    }
                    catch (InvalidPathException ipe)
                    {
                        MainWindow.logger.log(Level.SEVERE, ipe.getMessage(), ipe);
                    }
                }
                Gson gson = new GsonBuilder().create();
                return gson.toJson(createJsonData(pw.getRoot()));
            }
            catch (Exception e)
            {
                handleException(e);
            }
            return "";
        }
        public void handleException(Exception e)
        {
            MainWindow.logger.log(Level.SEVERE, "Unable to count files:"+e.getMessage(), e);
            Errors.addError("Unable to count files:"+e.getMessage());
            MainWindow.logger.log(Level.SEVERE, e.getMessage());
            Counters.getErrors().getCounter().incrementAndGet();
            SongKong.refreshProgress(FixSongsCounters.SONGS_ERRORS);
        }
        /**
         * Add this node and recursively its children,  returning json data representing the tree
         *
         * @param node
         * @return
         */
        private Data createJsonData(PathWalker2.Node node)
        {
            Data data = new Data();
            if(node.getFullPath()!=null)
            {
                data.setId(node.getFullPath().toString());
                if(node.getFullPath().getFileName()!=null)
                {
                    MainWindow.logger.severe("AddingNode(1):"+node.getFullPath().getFileName().toString());
                    data.setText(node.getFullPath().getFileName().toString());
                }
                else
                {
                    MainWindow.logger.severe("AddingNode(2):"+node.getFullPath().toString());
                    data.setText(node.getFullPath().toString());
                }
            }
            else
            {
                try
                {
                    data.setText(java.net.InetAddress.getLocalHost().getHostName());
                    data.setId("#");
                    State state = new State();
                    state.setOpened(true);
                    data.setState(state);
                }
                catch(UnknownHostException uhe)
                {
                    data.setText("Server");
                }
            }
            //Recursively add each child folder of this node
            Map<String, PathWalker2.Node> children = node.getChildren();
            if(children.size()>0)
            {
                data.setChildren(new ArrayList<>());
                for (Map.Entry<String, PathWalker2.Node> next : children.entrySet())
                {
                    data.getChildren().add(createJsonData(next.getValue()));
                }
            }
            else
            {
                data.setBooleanchildren(true);
            }
            return data;
        }
        public static String createFolderJsonData(Request request, Response response)
        {
            if(Strings.nullToEmpty(request.queryParams("id")).equals("#"))
            {
                CreateFolderTree cft = new CreateFolderTree(null);
                String treeData = cft.start(1).replace("booleanchildren", "children");
                return treeData;
            }
            else
            {
                CreateFolderTree cft = new CreateFolderTree(Paths.get(request.queryParams("id")));
                String treeData = cft.start(2    ).replace("booleanchildren", "children");
                return treeData;
            }
        }
    }
    import java.nio.file.Path;
    import java.util.Collections;
    import java.util.Map;
    import java.util.TreeMap;
    /** Constructs a tree of folders based on a list of filepaths
     *
     * i.e a give it a list if all folder that  contain files that have been modified and it creates a hierachy
     * that can then be used to generate a data structure for use by jstree
     *
     */
    public class PathWalker2
    {
        private final Node root;
        public PathWalker2()
        {
            root = new Node();
        }
        public Node getRoot()
        {
            return root;
        }
        /**
         * Represent a node on the tree (may/not have children)
         */
        public static class Node
        {
            //Keyed on name and node
            private final Map<String, Node> children = new TreeMap<>();
            private Path fullPath;
            public Node addChild(String name)
            {
                if (children.containsKey(name))
                    return children.get(name);
                Node result = new Node();
                children.put(name, result);
                return result;
            }
            public Map<String, Node> getChildren()
            {
                return Collections.unmodifiableMap(children);
            }
            public void setFullPath(Path fullPath)
            {
                this.fullPath = fullPath;
            }
            public Path getFullPath()
            {
                return fullPath;
            }
        }
        /**
         * @param path
         */
        public void addPath(Path path)
        {
            Node node = root.addChild((path.getRoot().toString().substring(0, path.getRoot().toString().length() - 1)));
            //For each segment of the path add as child if not already added
            for (int i = 0; i < path.getNameCount(); i++)
            {
                node = node.addChild(path.getName(i).toString());
            }
            //Set full path of this node
            node.setFullPath(path);
        }
    }
 
     
     
    