Hello,
Attached is a simple script exposing a possible bug when git alias is combined with git commands in script. It should be pretty self-explanatory. Check what it does and execute it. On my Linux and OSX, both with git 2.5.1 behave the same, ie. git add fails even the file "test" is in $PWD.
Summary: $GIT_WORK_TREE persists in env, and then some git commands operate on repo in $PWD (like git log), while some others (like git add) operate on repo in $GIT_WORK_TREE, making it inconsistent and results in very unexpected results.
Cheers, Tuomo