Clean working directory after fetching the config

src/com/sheepit/client/Client.java

@@ -130,8 +130,6 @@ import okhttp3.HttpUrl;
 			step = this.log.newCheckPoint();
 			this.gui.status("Starting");
 			
-			this.configuration.cleanWorkingDirectory();
-			
 			Error.Type ret;
 			ret = this.server.getConfiguration();
 			
@@ -162,6 +160,9 @@ import okhttp3.HttpUrl;
 				}, this.configuration.getShutdownTime());
 			}
 
+			// Check integrity of all files in the working directories
+			this.configuration.cleanWorkingDirectory();
+
 			this.startTime = new Date().getTime();
 			this.server.start(); // for staying alive
 			
@@ -508,7 +509,6 @@ import okhttp3.HttpUrl;
 			}
 		}
 
-		// 		this.configuration.workingDirectory.delete();
 		this.configuration.removeWorkingDirectory();
 		
 		if (this.server == null) {