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/CoffeeFile.java

@@ -0,0 +1,143 @@
+/*
+ * 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.*;
+
+public class CoffeeFile {
+	protected CoffeeFS coffeeFS;
+	protected CoffeeHeader header;
+	private String name;
+	private int length;
+	private int reservedSize;
+	private CoffeeMicroLog microLog;
+	private boolean knownLength;
+
+	public CoffeeFile(CoffeeFS coffeeFS, CoffeeHeader header) throws IOException {
+		this.coffeeFS = coffeeFS;
+		this.header = header;
+		name = header.name;
+		reservedSize = header.maxPages * coffeeFS.getConfiguration().pageSize;
+		if (header.isModified() && 
+		   coffeeFS.getConfiguration().useMicroLogs == true) {
+			microLog = new CoffeeMicroLog(coffeeFS, coffeeFS.readHeader(header.logPage));
+		} else {
+			microLog = null;
+		}
+	}
+
+	private int calculateLength() throws IOException {
+		byte[] bytes = new byte[1];
+		int i;
+
+		for (i = reservedSize; i >= header.rawLength(); i--) {
+			coffeeFS.getImage().read(bytes, 1, header.getPage() * coffeeFS.getConfiguration().pageSize + i);
+			if (bytes[0] != 0) {
+				return i - header.rawLength() + 1;
+			}
+		}
+		return 0;
+	}
+
+	public void insertContents(FileInputStream input) throws IOException {
+		byte[] bytes = new byte[1];
+		int ch;
+		int startOffset = header.getPage() *
+				  coffeeFS.getConfiguration().pageSize +
+				  header.rawLength();
+
+		length = 0;
+		knownLength = true;
+
+		while((ch = input.read()) != -1) {
+			bytes[0] = (byte) ch;
+
+			coffeeFS.getImage().write(bytes, 1,
+				startOffset + length);
+			length++;
+		}
+	}
+
+	public void saveContents(File file) throws IOException {
+		int startOffset = header.getPage() *
+				  coffeeFS.getConfiguration().pageSize +
+				  header.rawLength();
+		int i;
+		byte[] bytes;
+
+		FileOutputStream fOut = new FileOutputStream(file);
+
+		if (microLog != null) {
+			for (i = 0; i < microLog.getLogRecords(); i++) {
+				bytes = microLog.getRegion(i);
+				if (bytes == null) {
+					bytes = new byte[microLog.getLogRecordSize()];
+					coffeeFS.getImage().read(bytes, bytes.length, i * microLog.getLogRecordSize());
+				}
+				fOut.write(bytes);
+			}
+		} else {
+			bytes = new byte[1];
+			for (i = 0; i < getLength(); i++) {
+				coffeeFS.getImage().read(bytes, 1, startOffset + i);
+				fOut.write(bytes);
+			}
+		}
+
+		fOut.close();
+	}
+
+	public void remove() {
+		header.makeObsolete();
+	}
+
+	public CoffeeHeader getHeader() {
+		return header;
+	}
+
+	public int getLength() throws IOException {
+		if (!knownLength) {
+			length = calculateLength();
+			knownLength = true;
+		}
+		return length;
+	}
+
+	public String getName() {
+		return name;
+	}
+
+	public int getReservedSize() {
+		return reservedSize;
+	}
+}