BUG: setup.py does not allow equal filenames in *different* directories
Is it possible to write tests for setup.py?
## Setup

```
touch pandas/period.pyx
```

and put this in your `setup.py`'s ext_data:

``` python
    period=dict(pyxfile='period'),
```
## Before PR

``` bash
python setup.py build_ext --inplace
rm -rf pandas/period.c
python setup.py build_ext --inplace
python setup.py clean 
ls -l pandas/period.c
# -rw-rw-r-- 1 brandon brandon 48253 Feb  4 15:27 pandas/period.c
```

`period.c` still exists after cleaning.
## After PR

``` bash
python setup.py build_ext --inplace
rm -rf pandas/period.c
python setup.py build_ext --inplace
python setup.py clean
ls -l pandas/period.c   
# ls: cannot access pandas/period.c: No such file or directory
```
