I was using 2.16 version and everything was alright, I could merge two layers via Vector - Data Management - Merge and use .shp format as saved output format. Unfortunately my working laptop was reinstalled and now when I installed same QGIS back - I can't use this .shp option (I have only dbf, csv, xlsx and ods) and it really drives me crazy. I removed 2.16 and replaced with 2.18 but still have same issue. I 2.16 I could at least use SAGA merge tools for it but in 2.18 I can't.
I am trying to merge and save two layers (shp with same geometry type and CRS).
Add: I tried to download QGIS 2.18.4, removed all registry files and every single file related to QGIS to make sure I don' t have any hidden setting in Windows folders but it didn't help.
I looked into all QGIS Settings I found and I just can't see anything related to it.
Tried Vector menu, Processing Toolbox and nothing.