Considering application.conf is properties file. There is other option, which can solve the same purpose of using properties file.
Not sure but packaging properties file with jar might not provide flexibility? Here keeping properties file separate from jar packaging, this will provide flexibility as, whenever if any property changes just replace new properties file instead of building and deploying whole jar.
This can be achieved as, keep your properties in properties file are prefix your property key with "spark."
spark.inputpath /input/path
spark.outputpath /output/path
Spark Submit command would be like,
$spark_submit $spark_params $hbase_params \
--class com.abc.xyz.MYClass \
--properties-file application.conf \
$sandbox_jar flagFile/test.FLG
Getting properties in code like,
sc.getConf.get("spark.inputpath") // /input/path
sc.getConf.get("spark.outputpath") // /output/path
Not nessesary it will solve your problem though. But here just try to put another approach to work.