allow to customize timeout and env vars for program based hooks

Fixes #847

Signed-off-by: Nicola Murino <nicola.murino@gmail.com>

cmd/startsubsys.go

@@ -111,6 +111,11 @@ Command-line flags should be specified in the Subsystem declaration.
 				logger.Error(logSender, connectionID, "unable to initialize http client: %v", err)
 				os.Exit(1)
 			}
+			commandConfig := config.GetCommandConfig()
+			if err := commandConfig.Initialize(); err != nil {
+				logger.Error(logSender, connectionID, "unable to initialize commands configuration: %v", err)
+				os.Exit(1)
+			}
 			user, err := dataprovider.UserExists(username)
 			if err == nil {
 				if user.HomeDir != filepath.Clean(homedir) && !preserveHomeDir {