Cleanup PATHs before changing them

Trying to clean the PATH and MANPATH before change them.
I think this is going to cause problems when `php-config --prefix` evaluates to something like `/usr`. In that case, the user would end up losing the following items out of `$PATH`:

```
/usr/bin
/usr/libexec
/usr/local/MacGPG2/bin
/usr/local/bin
/usr/local/sbin
/usr/sbin
```