Enhance import error reporting

This PR
* breaks the sra import code into more functions
* does extra error checking around chdir(), the validation helper, and around shellcmd()
* also adds logic to handle the case where bam has an alignment but no unaligned reads
This isn't something changed in this PR, but would it be better to `Genome::Model::Tools::Picard::FastqToSam->execute()` directly?