doxygen update + Driver directory rename

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Georg
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</ol>
<p>In either way, the ChameleonMini now jumps to the bootloader and waits patiently for a firmware upgrade.</p>
<h1>Step 2: Upgrade the Firmware </h1>
<p>Once the ChameleonMini is in the bootloader, you can flash a new firmware, i.e., the files <a href="https://cdn.rawgit.com/emsec/ChameleonMini/master/Firmware/Chameleon-Mini/Chameleon-Mini.hex">Chameleon-Mini.hex</a> and the <a href="https://cdn.rawgit.com/emsec/ChameleonMini/master/Firmware/Chameleon-Mini/Chameleon-Mini.eep">Chameleon-Mini.eep</a>, into the microcontroller. The source code directory contains these files precompiled but you can of course also compile the code yourself. Create a new folder and copy the two files into it. The following depends on your operating system:</p>
<p>Once the ChameleonMini is in the bootloader, you can flash a new firmware, i.e., the files <a href="https://cdn.rawgit.com/emsec/ChameleonMini/master/Firmware/Chameleon-Mini/Latest/Chameleon-Mini.hex">Chameleon-Mini.hex</a> and the <a href="https://cdn.rawgit.com/emsec/ChameleonMini/master/Firmware/Chameleon-Mini/Latest/Chameleon-Mini.eep">Chameleon-Mini.eep</a>, into the microcontroller. The source code directory contains these files precompiled but you can of course also compile the code yourself. Create a new folder and copy the two files into it. The following depends on your operating system:</p>
<h2>Upgrade Procedure for Linux Users</h2>
<p>In order to upgrade the firmware under Linux you first have to install <code>avrdude</code>, e.g. under Ubuntu with the command <code>sudo apt-get install avra avrdude</code>. Then change to the directory where you have saved the hex and eep files and run <code>sudo avrdude -c flip2 -p ATXMega128A4U -B 60 -P usb -U application:w:Chameleon-Mini.hex:i -U eeprom:w:Chameleon-Mini.eep:i</code>.</p>
<p>You also can use <code>sudo make program</code> in the source code directory, which basically does the same.</p>
<p>After running this command you need to restart your Chameleon, e.g. by reattaching the Chameleon to the PC.</p>
<dl class="section note"><dt>Note</dt><dd>If you are using Ubuntu 14.04, avrdude may not support flip2. In this case, you can run <code>add-apt-repository ppa:pmjdebruijn/avrdude-release</code>, then <code>apt-get update</code> and finally <code>apt-get install avrdude</code> to upgrade to a version of avrdude that supports flip2.</dd></dl>
<p>Optionally copy Drivers/98-ChameleonMini.rules to /etc/udev/rules.d/, to allow non-root users to open the chameleon serial port at /dev/chameleon. <code>sudo cp (Path to Chameleon Repo)/Drivers/98-ChameleonMini.rules /etc/udev/rules.d/</code> Remember to restart the udev daemon, or reboot to activate the rule. 'sudo udevadm control &ndash;reload'</p>
<p>Optionally copy <a href="https://cdn.rawgit.com/emsec/ChameleonMini/master/Drivers/98-ChameleonMini.rules">Drivers/98-ChameleonMini.rules</a> to /etc/udev/rules.d/, to allow non-root users to open the chameleon serial port at /dev/chameleon. <code>sudo cp (Path to Chameleon Repo)/Drivers/98-ChameleonMini.rules /etc/udev/rules.d/</code> Remember to restart the udev daemon, or reboot to activate the rule. 'sudo udevadm control &ndash;reload'</p>
<h2>Upgrade Procedure for Mac OS Users</h2>
<p>When running <a href="https://brew.sh">Homebrew</a> you can install avrdude with <code>brew install avrdude</code>. After this, change to the directory where you have saved the hex and eep files and run <code>sudo avrdude -c flip2 -p ATXMega128A4U -B 60 -P usb -U application:w:Chameleon-Mini.hex:i -U eeprom:w:Chameleon-Mini.eep:i</code>.</p>
<h2>Upgrade Procedure for Windows Users</h2>
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<li>Save the <a href="https://cdn.rawgit.com/emsec/ChameleonMini/master/Firmware/Chameleon-Mini/ChameleonFirmwareUpgrade.bat">ChameleonFirmwareUpgrade.bat</a> in the same directory as the hex and eep files.</li>
<li>Run the <code>ChameleonFirmwareUpgrade.bat</code> as Administrator (right click -&gt; run as Administrator) and wait for the firmware upgrade to terminate. Upon success, the green LED of the ChameleonMini should light up.</li>
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<p>Finally, install the driver for Chameleon: Download both <a href="https://cdn.rawgit.com/emsec/ChameleonMini/master/Driver/ChameleonDriver.inf">ChameleonDriver.inf</a> and <a href="https://cdn.rawgit.com/emsec/ChameleonMini/master/Driver/ChameleonDriver.cat">ChameleonDriver.cat</a> from the Drivers directory and install the INF file (right click -&gt; install).</p>
<p>Finally, install the driver for Chameleon: Download both <a href="https://cdn.rawgit.com/emsec/ChameleonMini/master/Drivers/ChameleonDriver.inf">ChameleonDriver.inf</a> and <a href="https://cdn.rawgit.com/emsec/ChameleonMini/master/Drivers/ChameleonDriver.cat">ChameleonDriver.cat</a> from the Drivers directory and install the INF file (right click -&gt; install).</p>
<p>Now, Chameleon should appear in the Windows device manager and you should be able to open a terminal program such as TeraTerm and connect to the Chameleon-Mini via the COM port shown in the device manager. On Mac or Linux you can use screen (<code>screen /dev/tty.usbmodem1421</code>, please replace your device path with the appropriate one) to communicate with your Chameleon. Further information about how to "talk" to the Chameleon can be found here: <a class="el" href="Page_CommandLine.html">The Chameleon Command Structure</a>. </p>
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