copy app config, use new pt config, clean dir

Previously we used deployDir/targetDir/config.json for the paratrooper config, but now this is paratrooper.json in the same location. If that file doesn't exist, it renames the old config.json to permanently convert it (once 1.0 hits, the conversion will be removed).

Now if you place a config.json in you target directory, it will be copied to [appPath]/server/config.json or if the [appPath]/server/ folder doesn't exist, then just to the root folder (appPath).

Also cleans up the project directory before doing a pull (git clean -xdf).