Add missing args to initETE3Database

[dfornika]

Fixes #141

I've standardized all call sites to initETE3Database() to pass database_directory and ETE3DBTAXAFILE.

I've also added database_directory as an argument to NamesToTaxIDs(), so it can be passed along to initETE3Database().

I've also modified the function signatures and call sites to other functions that call initETE3Database():

• getHeirarchy()
• getTaxid()
• getTaxonConvergence()

I've removed logging as an argument to initETE3Database() as it doesn't appear to be necessary.