Changed from using the deprecated functions in the os module to using the
new ones in the subprocess module. All string reading now also uses the
string.decode() function, which seems to be recommended practice whenever
the input is a little "iffy".
To accommodate this modification, the changing of working directory (when
a repository is specified) has been moved from the system module to the
main gitinspector module. This enables us to change directory in one go
when gitinspector starts, thus removing the need for the previous system
module.
If any missing files are detected during analysis, gitinspector reports them
in a list. If, on the other hand, the --checkout-missing option is supplied,
gitinspector will try to checkout any missing files instead.
