Change superkingdom to domain in default taxonomic levels to match NCBI changes

• Catch 404 errors and report as errors
• Add resume argument to download functions
• Don't retain temp files for downloads if less than 10kb
• README touchups

• Fix bug in testing script

• Allow factors as input to accessionToTaxa
• Document sqlite pragmas for read.accession2taxid
• Inherit ... argument documentation for prepareDatabase
• Catch input/output error while processing large files
• Update various user-facing links from ftp to https for easier access
• Add quote option to makeNewick
• Trim trailing NAs off the tree in makeNewick if excludeTerminalNAs is TRUE
• Add terminal semicolon to end of makeNewick tree unless terminator is NULL
• Add "no rank" to normalizeTaxa's default exclusion
• Expand README
• Add normalizeTaxa function

• Add getRawTaxonomy function to pull complete taxonomy for a given taxa
• Compare md5 of files after download to the md5 provided by NIH to ensure file integrity
• Deal with Windows download/md5 issues
• Add option to only prepare the names and nodes taxonomy part of the database for people that do not need to process accession IDs

• Switch to curl package for downloading
• Add curl package dependency (necessary to avoid download.file() issues on Windows)
• Remove option('timeout') settings since not used in curl
• This should fix the strange download issues that have been reported on Windows e.g. issues #27, #28, #31

• Deal with R's default download timeout of 60 seconds
• Fix named vector bug
• Add makeNewick function
• Fix warnings in dbConnect, untar and example output

• Remove nucl_est and nucl_gss from defaults since NCBI folded them into nucl_gb and removed
• Squash R:devel bug
• Update README

• Transitioned from data.table to SQLite
• Added convenience prepareDatabase() function
• Squashed Windows testing errors