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In the original ZBrowse, the user had to specify the organism by hand, but now we infer the correct organism from the dataset.

Append to Current Dataset
If checked, this combines all requested traits (local and remote) into the currently selected dataset. (I prefer doing it this way.)
If unchecked, it ignores the current dataset, loads each trait into a separate dataset, and displays one of these. (This is the default, for consistency with the original ZBrowse.)

The default (Medicago truncatula GWAS and Arabidopsis thaliana GWAS) datasets contain no traits (at first), allowing you to stock them (with Append to Current Dataset checked) from local or remote files.

Local Trait Files: Browse button
For "JavaScript security reasons", there appears to be no way to clear the display of which local files are scheduled to be loaded. However, changing the dataset should correctly clear the local file list in the background.