Let fetch script be able to fetch both query or hit

Additional parameter added. Specify either "query" or "hit". With "hit" the script fetches all hit sequences (as it did before). With "query" you can now also fetch the query sequences.
Rename fetch script: fetchBlastSequences.py
Bugfixes in makefile
Bugfix in fetchBlastSequences
Reset file permissions after system migration
Make rm commands in Makefile more explicit
Increase number of BLAST threads
Bugfix in fetchBlastSequences
Update notes