for the module with osgi facet change manifest using option to 'manually edited'. Choose not to use project-default manifest location but don't specify any path in the corresponding field.
You get the promting dialog:
The manifest file /MANIFEST.MF was not found. Should it be created now?
Press yes and close project settings dialog.
The prompting dialog appears again. Try to close it by selecting 'yes' – no results: dialog appears again and again.
Press 'no' : after few attempts dialog is closed.
File is created in the module root (but dialog appears again on project reopening etc)