I run motodev studio 1.3 and could not make a Java project from exist souce code. here is an alternative ways to do so.
1. Compile the Android project
cd /path/to/android/root
make # and wait a while, if you haven't done this
(Any problem, Refer to http://blog.csdn.net/pengmens/archive/2010/11/02/5981762.aspx )
2. Make the "Java build path"
cd your_android_root_path
cp your_android_root_path/development/ide/eclipse/.classpath ./
chmod u+w .classpath # Make the copy writable
3. Download eclipse 3.5 and untar the download file
4. run eclipse
1). If Eclipse asks you for a workspace location, choose the default
2). If you have a "Welcome" screen, close it to reveal the Java perspective.
3). File > New > Java Project
4). Pick a project name, "AndroidSourceProject" or anything you like.
5). Select "Create project from existing source" (MOTODEV hasn't the choice), enter the path to your Android root directory, and click Finish.
6).Wait while it sets up the project. (You'll see a subtle progress meter in the lower right corner.)
Here, you can navigate code inside the new created "AndroidSouceProject".
Of course, you can create new android project, when you try to "Open Declaration" after you right clicked at method/class, there would be a page lead you to make the AndroidSouceProject as link source.
And more, if you close the eclipse and run motodev with same workspace, sure their would be same.
Reference: https://sites.google.com/a/android.com/opensource/using-eclipse