Feature/cleanout files

Validated moa steps all run, the first throws an err in moa

```
cd gbs_moa/00_AlignerIndices
moa run
```

due to warning but appears to work

```
$  moa err | tail -n 4
2014-10-29 09:38:16 (249 KB/s) - `GBS_Workshop_Maize.zip' saved [359665756]

warning:  stripped absolute path spec from /
mapname:  conversion of  failed
```