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/CoffeeMicroLog.java

@@ -0,0 +1,95 @@
+/*
+ * 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.IOException;
+
+public class CoffeeMicroLog extends CoffeeFile {
+	private int logRecords;
+	private int logRecordSize;
+	private int indexStart;
+	private int indexSize;
+	private int recordStart;
+	private int[] index;
+
+	public CoffeeMicroLog(CoffeeFS fs, CoffeeHeader header)
+			throws IOException {
+		super(fs, header);
+
+		CoffeeConfiguration conf = fs.getConfiguration();
+		if (header.logRecordSize == 0) {
+			logRecordSize = conf.pageSize;
+		}
+		if (header.logRecords == 0) {
+			logRecords = conf.defaultLogSize / logRecordSize;
+		} else {
+			logRecords = header.logRecords;
+		}
+
+		indexStart = header.getPage() * conf.pageSize +
+			     header.rawLength();
+		/* An index entry uses two bytes. */
+		indexSize = logRecords * 2;
+		recordStart = indexStart + indexSize;
+
+		index = new int[logRecords];
+		byte[] bytes = new byte[2];
+
+		for (int i = 0; i < logRecords; i++) {
+			coffeeFS.getImage().read(bytes, bytes.length,
+				indexStart + i * 2);
+			index[i] = bytes[1] << 8 | bytes[0];
+		}
+	}
+
+	public byte[] getRegion(int region) throws IOException {
+		for (int i = logRecords - 1; i >= 0; i--) {
+			if (index[i] - 1 == region) {
+				byte[] bytes = new byte[logRecordSize];
+				coffeeFS.getImage().read(bytes, bytes.length, 
+					recordStart + i * logRecordSize);
+				return bytes;
+			}
+		}
+
+		return null;
+	}
+
+	public int getLogRecords() {
+		return logRecords;
+	}
+
+	public int getLogRecordSize() {
+		return logRecordSize;
+	}
+}