gradle.propertiesに定義した値をJavaソースから参照する ref: http://qiita.com/shts/items/d94834437b22712415c5

.gitignore

# BuildConfig.java を公開しないようにするため
/build
# gradle.properties を公開しないようにするため
gradle.properties

build.gradle

buildTypes {
    debug {
        buildConfigField "String", "PARSE_API_ID", "\"${project.property("parseApiId")}\""
        buildConfigField "String", "PARSE_API_KEY", "\"${project.property("parseApiKey")}\""
    }
    release {
        buildConfigField "String", "PARSE_API_ID", "\"${project.property("parseApiId")}\""
        buildConfigField "String", "PARSE_API_KEY", "\"${project.property("parseApiKey")}\""
        minifyEnabled false
        proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.pro'
    }
}

BuildConfig.java

public final class BuildConfig {
  // Fields from build type: debug
  public static final String PARSE_API_ID = "xxxxxxxxxxxxxxxxxxxxx";
  public static final String PARSE_API_KEY = "xxxxxxxxxxxxxxxxxxxxx";
}

file2.groovy

buildConfigField "String", "PARSE_API_ID", "\"${project.property("parseApiId")}\""
buildConfigField "String", "PARSE_API_KEY", "\"${project.property("parseApiKey")}\""

gradle.properties

parseApiId=xxxxxxxxxxxxxxxxxxxxx
parseApiKey=xxxxxxxxxxxxxxxxxxxxx

MyApplication.java

public class MyApplication extends Application {

    public MyApplication() {
        super();
    }

    @Override
    public void onCreate() {
        super.onCreate();
        Parse.initialize(this, BuildConfig.PARSE_API_ID, BuildConfig.PARSE_API_KEY);
        ParseInstallation.getCurrentInstallation().saveInBackground();
    }

}