define_resource_inputs copies input files

The `define_resource_inputs` rule copies input files to:
```
A/
T/
R/
G/
```

For examples, in case of `eval_resources.smk`, `R/` and `G/` will just have one copy of the same query file each. If the query file is big enough, this can be problematic. Since output files for rules can be symlinks, we should use them instead.