Output is not relative to base-path

[theofidry]

If you have something like:

{
    "output": "build/foo.phar",
    "main": "bin/foo.php",
    "base-path": "src"
}

Then the real path of the main used is $CWD/src/bin/foo.php and the output should be $CWD/src/build/foo.phar but actually is $CWD/build/foo.phar.