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@Michael Davidovich 
Refreshing the explorer only refreshes the nodes in the tree view. If you have a virtual file open that you opened from the explorer it won't auto-update. You can close it and reopen it and the extension should fetch the new copy. If you have your local copy open, you can export again to get the latest version.

@Michael Davidovich 
If you have a local folder open there should be two tree views within the ObjectScript view container (the left pane that is shown after clicking the InterSystems logo in the activity bar on the far left). The bottom one is the Projects Explorer and it's only used to create/modify/export server-side project contents (also known as Studio Projects). The top tree (with the Explorer name) is the ObjectScript Explorer where you can Compile/Export/Delete packages and files. Since you don't use server-side source control and need files in your local file system, you can safely ignore the Projects Explorer since they won't be useful for your workflow. Here's a screenshot of what this looks like for me in a locla folder called "langauge-server":

EDIT: If the ObjectScript Explorer isn't showing, make sure you don't have the setting "objectscript.showExpolorer" set to false.

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