By default, DITA2Go generates manifest file plugin.xml for Eclipse Help. If your workflow does not require generating this file because it is produced by some other process, you can exclude plugin.xml from your DITA2Go project.
To direct DITA2Go not to produce plugin.xml:
[EclipseHelpOptions] ; UsePlugin = Yes (default), or No (never write plugin.xml, use if ; not part of the deliverable system because others provide it) UsePlugin = No