"--basedir" option is not working

Currently, if the job file `job.json` looks like:
```
{
"input_file": {
"class": "File",
"path": "hello.txt"
}
}
```
Then `hello.txt` must be in placed in the same directory with `job.json`. With `--input-dir` option one could specify a base path other than the parent directory of `job.json` to resolve file inputs with relative paths. With that, one can place `job.json` and file inputs separately and independently of one another.