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From my testing, it only seems to occur when there are 2 dots in the source file name.
So either using mv, or renaming some of the intermediate files to only have one dot in the name 
should work.

Tor Lillqvist wrote:
$ touch soffice.bin.exe
$ cp soffice.bin.exe soffice.bin
cp: cannot create regular file `soffice.bin': File exists
mv, however, works...:

$ touch soffice.bin.exe
$ mv soffice.bin.exe soffice.bin
$ ls -l soffice*
-rw-r--r-- 1 tml None 0 Sep 21 17:50 soffice.bin

--tml


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