THe deployment directory is cleaned and this cannot be prevented.
I'm assuming that you are adding stuff in this directory that you need in your application.
To achieve the disered result you can use the resources directory in the project directory to add additional files or depending on the function you are trying to accomplish you can use the lib directory for java jar files, widget directory for new widgets, theme directory for ccs related stuff. THese will be copied to the delppoyment directory when running the application.