The removal of the option to upload the 'Other MS Document' type in the Implementation Report (IGJ, ETC & EMFF) was requested by DG EMPL and REGIO, and implemented in March 2016.
Information should be included in the Report itself as Structured data (via the tables or text-boxes).
If additional information is requested by your Desk Officer at the Commission, the sent version should be returned for modification by the EC in order for you to modify the information in the Structured data.