With the latest release of the Intel XDK (2496 and above) you should no longer be putting plugins inside the "source directory" (typically named "www") in your project directory AND you should no longer be referencing plugins via the intelxdk.config.additions.xml file. While this practice works with prior versions of the Intel XDK, it will cause problems with the current and future versions of the Intel XDK.
This change in policy is due to a significant change in the way the Intel XDK handles Cordova plugins. Unfortunately, the project upgrade process does not always detect all of these plugin references (especially plugins that are referenced via the intelxdk.config.additions.xml file) and may fail to include them in the Plugin Management section of the Projects tab.
For more information, please read this post: https://software.intel.com/en-us/forums/intel-xdk/topic/594986
p.s. The build system will still attempt to pull in plugins that are referenced in the intelxdk.config.additions.xml file, which can cause conflicts with plugins you have added via the plugin manager.
p.p.s. We are aware that many older forum posts (and a few doc pages that need to be updated) may recommend using the intelxdk.config.additions.xml file for referencing plugins, that was appropriate with older versions of the Intel XDK but is no more. We are working on updates to the documentation to minimize any confusion.
