Replace temp with method (custom_annotation_inputs)
Replace temp with method (vep_params)
Replace temp with methods
Remove spurious execution return value checking
Add SplitAlternateAlleles and test

This command splits vcf lines into multiple lines (one per alternate
allele) and clears INFO fields.
Fix imports related to File::Vcf::Differ
Vep correctly annotates multiple alternate alleles
Invalid annotation plans cause builds to be unstartable
Use Genome::Sys->shellcmd instead of IPC::Run

1) for status logging
2) for input/output file validation
die when no API path can be found

This makes it so that less boilerplate is needed by consumers of this
method as well as being more consistent with the way Sys->shellcmd
works.