mixing of errors and output if output goes to stdout

If --outfile is not specified error messages and output are mixed. This is because some messages also go to stdout: 

- `. 26 sites are made from completely undetermined states ('X', '-', '?' or 'N')...`
- ```
. 0.000010 0.000001 0.000001 0.000001
. 0.000000 -- -3.616917
. Err. in Optimize_Br_Len_Serie
. Type any key to exit.
```


