This is not only about ignored files, but untracked files. And the check
is already there: git said:
Untracked working tree file 'Project/bin/path/file.jjt' would be
overwritten by merge.
Well the meaning of the error message is clear to you but it wasn't
for me. I simply would not ask if I knew how to correctly interpret
it. I hope I'll have a time to make a little improvement here...
Bost
PS: ...and you can reject it if you don't agree :-)