A method for debugging an application running on a target device includes running a debugging program on a host device. A global path substitution is specified, the global path substitution indicating a first file path according to a file path convention of the host device to be substituted for a second file path according to a file path convention of the target device. The path substitution avoids file path ambiguities which may occur, for example, when the host attempts to access files having file paths referenced to the file path convention of the target device.