Did you write it to be run from anywhere, or inside it does it call programs by relative path such as 'program' instead of '/me/program' and it now cannot find them?
Run your shell script as bash -x /me/script.sh and see what's going wrong. There's no overall technical reason a script can't work outside your directory, so it's got to be something you're running that expects $CWD to be /me.
What error does it give you?
Did you write it to be run from anywhere, or inside it does it call programs by relative path such as 'program' instead of '/me/program' and it now cannot find them?
Run your shell script as
bash -x /me/script.shand see what's going wrong. There's no overall technical reason a script can't work outside your directory, so it's got to be something you're running that expects$CWDto be/me.