It's easiest to use the build_skymap.sh script in the parent directory, but if you want to understand the steps:

The following procedure will regenerate the binary star data:

1. Build the utilities with ./gradlew assemble installDist from the stardroid directory.
2. Gradle's application plugin generates the wrong classpath for the utilities. Fix it by going into tools/build/install/datagen/bin/datagen and removing the apk from the classpath. Leave the root installation directory $APP_HOME/lib.
3. Convert the star and messier data files to text protocol buffers with ./generate.sh from the tools directory.
4. Finally run ./binary.sh from the tools directory to convert the ascii proto bufs to binary ones (and put them in the right directory).