Fix #665 autoHotswap and disabledPlugins does not work when using external hotswap-agent.properties

Author: skybber

hotswap-agent-core/src/main/java/org/hotswap/agent/config/PluginConfiguration.java

@@ -98,6 +98,8 @@ private void loadConfigurationFile() {
             if (externalPropertiesFile != null) {
                 configurationURL = resourceNameToURL(externalPropertiesFile);
                 properties.load(configurationURL.openStream());
+                containsPropertyFileDirectly = true;
+                properties.putAll(System.getProperties());
                 return;
             }