So I finally managed to figure out a little bit about how Josh's compiler works and was able to fix the issue with why definitions modified was populating keyword and function lists for the plugin with only those that were unscoped.
The following commit contains the fix.https://github.com/RobertBColton/enigma-dev/commit/3a3d863e88d65fc8ec9ab4b836a2cceb5e098418
I have also partially corrected the issue with them not showing up properly in the Function List panel and the autocompletion window.
The following is the commit to the LGM plugin that resolves this.https://github.com/enigma-dev/lgmplugin/commit/e82762d65e0b47f41cfcf3d240948d1344d95941
As you can see in the following image not only does it display correct but ENIGMA specific functions such as those for threads will now syntax highlight.
While I am on the subject, this window from the plugin should have access to all definitions and be able to filter them, for debugging purposes it is useful to look up definitions and tokens from other namespaces and what not. This could also all be done from a single window.
I created a mockup of what the frame could look like in Qt.