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[ BUILD # : 201109141017 ] [ JDK VERSION : 1.7 ] When it was part of the new Module wizard it listed the files that were modified as part of adding the layer file. For newbies, like me not so long ago, this at least gave some hints of what's going on the background and is the only way to know what to modify back if you need to remove it for some reason.
"Created Files" shows the layer; ought to also list manifest.mf under "Modified Files". At least that is I suppose what you were talking about; your description is hard to follow.
https://hg.netbeans.org/core-main/rev/9620568488bb
Fixed tests. https://hg.netbeans.org/core-main/rev/1a01bae3388c