After updating yesterday to the latest version of Windows sourcetree, I can no longer stage deleted files. I can stage changed and new files just fine.

I get this error every time I try to stage a deleted file:

git -c diff.mnemonicprefix=false -c core.quotepath=false rm -q -f – Upgrades.json
fatal: pathspec 'Upgrades.json' did not match any files

Completed with errors, see above.

As a workaround, I add the file from git command line and it then works to actually do the commit.

The path to my file in this case is actually "rules/Upgrades.json", and not simply "Upgrades.json" in the root folder, as the error message might suggest. Maybe you simply got the path wrong?