skip generate merged assemblies if we don't have a merged fasta file
remove unused/old code

We believe these were either never really used or were only used experimentally
so we are removing the code and archiving the database data.  If one of these
turns out to be needed then contact APIPE to coordinate a restore.

Related classes:

Genome::Disease
Genome::Model::BuildSV
Genome::Model::SV
Genome::Model::VariantSource
Genome::Model::VariantValidation
Genome::SNVManualReview
Genome::SequenceDiff
Genome::SequenceDiffEval
Genome::SequenceDiffPart
Genome::UpdateHistory
Genome::VRList
Genome::VRListMember
Genome::VariantOccurrence
Genome::VariantReviewDetail
Genome::VariantReviewDetailOld
Genome::VariantReviewList
Genome::VariantReviewListFilter
Genome::VariantReviewListMember

Related tables:

DISEASE
GENOME_MODEL_BUILD_SV
GENOME_MODEL_SV
GENOME_MODEL_VARIANT_SOURCE
GENOME_MODEL_VARIANTVALIDATION
SNV_MANUAL_REVIEW
SEQUENCE_DIFF
SEQUENCE_DIFF_EVAL
SEQUENCE_DIFF_PART
GENOME_VR_LIST
GENOME_VR_LIST_MEMBER
VARIANT_OCCURRENCE
VARIANT_REVIEW_DETAIL
VARIANT_REVIEW_DETAIL_OLD
VARIANT_REVIEW_LIST
VARIANT_REVIEW_LIST_FILTER
VARIANT_REVIEW_LIST_MEMBER
remove `gmt annotate genomic-regions`

Command produces warnings when used and appears to have almost no usage:

2010/06/15  dkoboldt  gmt annotate genomic-regions --help
2010/06/15  dkoboldt  gmt annotate genomic-regions --bed-file ... --output-directory ...
2010/06/02  ckandoth  gmt annotate genomic-regions
2010/06/02  ckandoth  gmt annotate genomic-regions --help
2010/06/02  ckandoth  gmt annotate genomic-regions --help
2010/06/29  kchen     gmt annotate genomic-regions
2010/06/30  wschierd  gmt annotate genomic-regions --help
2010/06/30  wschierd  gmt annotate genomic-regions --bed-file ... --output-directory ...
2010/07/02  wschierd  gmt annotate genomic-regions --help
2010/07/02  wschierd  gmt annotate genomic-regions --bed-file ... --output-directory ...
2010/07/02  wschierd  gmt annotate genomic-regions --bed-file ... --output-directory ...
2010/07/02  wschierd  gmt annotate genomic-regions --bed-file ... --output-directory ...
2010/08/11  jwalker   gmt annotate genomic-regions --help
2010/08/11  jwalker   gmt annotate genomic-regions --help
2011/01/12  jwallis   gmt annotate genomic-regions --help
2012/07/24  dmorton   gmt annotate genomic-regions --help
2013/07/10  jhundal   gmt annotate genomic-regions --help
Merge branch 'removal'
Updated class browser cache.
Updated `genome` tab completion.
Updated `gmt` tab completion.
Merge remote-tracking branch upstream/$:{upbranch}