Download deps: do not use log file

Since the download of sources are performed in parallel, we cannot use
anymore a single log file.

The output of the download commands has been reduced to errrors only and
it will be outputted directly on stderr. Thus the log file stuff have been
completely removed.

Moreover the clonedeps function now takes the REPO as second parameter
and additional (non mandatory) git flags as fourth parameter.

Additional fixes have been introduced to run commands in script mode
(-q, -f, ...)