When I run this command from terminal to identify file renames,

git add -A 

all the files are displayed in SourceTree correctly as renames, but after commit, all the renamed files will be staged again as removed. It will commit renames as new files and leave old file names as deleted. History between file renames will be broken and only way back is to hard reset head and do everything from command line.

git reset HEAD~ 

This is serious problem.