Renamed Java packages to match our contiki-os.org domain. Note that this commit does not affect external dependencies

like /tools/mspsim.

This is a very simple modification that affects a very large number of files in Contiki: Cooja,
/platform/cooja, Collect-view, Coffe-manager, and Cooja simulation files (.csc).

I've gone through Contiki to update all references I could find. Nevertheless, this commit will likely
break external dependencies, like saved Cooja simulation files.

tools/coffee-manager/org/contikios/coffee/CoffeeFS.java

@@ -0,0 +1,197 @@
+/*
+ * Copyright (c) 2009, Swedish Institute of Computer Science
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ * 3. Neither the name of the Institute nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ *
+ * @author Nicolas Tsiftes
+ *
+ */
+
+package org.contikios.coffee;
+
+import java.io.*;
+import java.util.Map;
+import java.util.TreeMap;
+
+public class CoffeeFS {
+	private final CoffeeImage image;
+	private final CoffeeConfiguration conf;
+	private int currentPage;
+	private Map<String, CoffeeFile> files;
+	private static final int INVALID_PAGE = -1;
+
+	public CoffeeFS(CoffeeImage image) throws IOException {
+		this.image = image;
+		conf = image.getConfiguration();
+		currentPage = 0;
+		files = new TreeMap<String, CoffeeFile>();
+
+		while(currentPage < (conf.fsSize / conf.pageSize)) {
+			CoffeeHeader header = readHeader(currentPage);
+			if (header.isActive() && !header.isLog()) {
+				CoffeeFile file = new CoffeeFile(this, header);
+				files.put(file.getName(), file);
+			}
+			currentPage = nextFile(header, currentPage);
+		}
+	}
+
+	private int pageCount(long size) {
+		int headerSize = conf.nameLength + conf.pageTypeSize * 2 + 6;
+		return (int)(size + headerSize + conf.pageSize - 1) / conf.pageSize;
+	}
+
+	private int findFreeExtent(int pages) throws IOException {
+		CoffeeHeader header;
+		int currentPage = 0;
+		int start = INVALID_PAGE;
+
+		while(currentPage < (conf.fsSize / conf.pageSize)) {
+			header = readHeader(currentPage);
+			if (header.isFree()) {
+				if (start == INVALID_PAGE) {
+					start = currentPage;
+				}
+				currentPage = nextFile(header, currentPage);
+				if (start + pages <= currentPage) {
+					return start;
+				}
+			} else {
+				start = INVALID_PAGE;
+				currentPage = nextFile(header, currentPage);
+			}
+		}
+		return INVALID_PAGE;
+	}
+
+	public CoffeeImage getImage() {
+		return image;
+	}
+
+	public CoffeeConfiguration getConfiguration() {
+		return conf;
+	}
+
+	public CoffeeHeader readHeader(int page) throws IOException {
+		byte[] bytes = new byte[conf.nameLength + conf.pageTypeSize * 2 + 6];
+
+		image.read(bytes, bytes.length, page * conf.pageSize);
+		CoffeeHeader header = new CoffeeHeader(this, page, bytes);
+
+		return header;
+	}
+
+	public void writeHeader(CoffeeHeader header) throws IOException {
+		byte[] bytes = header.toRawHeader();
+
+		image.write(bytes, bytes.length, header.getPage() * conf.pageSize);
+	}
+
+	private int nextFile(CoffeeHeader header, int page) {
+		if (header.isFree()) {
+			return page + conf.pagesPerSector & ~(conf.pagesPerSector - 1);
+		} else if (header.isIsolated()) {
+			return page + 1;
+		}
+
+		return page + header.maxPages;
+	}
+
+	public final Map<String, CoffeeFile> getFiles() {
+		return files;
+	}
+
+        public CoffeeFile insertFile(String filename) throws IOException {
+          return insertFile(new File(filename));
+        }
+        
+	public CoffeeFile insertFile(File file) throws IOException {
+	    CoffeeFile coffeeFile;
+	    FileInputStream input = new FileInputStream(file);
+	    int allocatePages = pageCount(file.length());
+	    int start = findFreeExtent(allocatePages);
+
+	    if (start == INVALID_PAGE) {
+	        input.close();
+	        return null;
+	    }
+	    CoffeeHeader header = new CoffeeHeader(this, start);
+	    header.setName(file.getName());
+	    header.setReservedSize(allocatePages);
+	    header.allocate();
+	    coffeeFile = new CoffeeFile(this, header);
+	    writeHeader(header);
+	    coffeeFile.insertContents(input);
+	    input.close();
+	    return coffeeFile;
+	}
+
+	public void removeFile(String filename)
+			throws CoffeeFileException, IOException {
+		CoffeeFile file = files.get(filename);
+		if (file == null) {
+			throw new CoffeeFileException("Coffee: attempt to remove inexistent file");
+		}
+
+		file.remove();
+		writeHeader(file.getHeader());
+		files.remove(file.getName());
+	}
+
+	public boolean extractFile(String filename) throws IOException {
+	  return extractFile(filename, new File(filename));
+	}
+	
+	public boolean extractFile(String fileInCoffee, File fileOnDisk) throws IOException {
+		CoffeeFile file = files.get(fileInCoffee);
+
+		if (file == null) {
+			return false;
+		}
+
+		file.saveContents(fileOnDisk);
+		return true;
+	}
+
+	public static class CoffeeException extends RuntimeException {
+		private static final long serialVersionUID = 1146474084441011154L;
+
+		public CoffeeException(String message) {
+			super("Coffee error: " + message);
+		}
+	}
+
+	public static class CoffeeFileException extends RuntimeException {
+
+		private static final long serialVersionUID = -2954553141887245203L;
+
+		public CoffeeFileException(String message) {
+			super("Coffee file error: " + message);
+		}
+	}
+
+
+}