Move sanger dump file system to site tgi sync sanger class
Remove gmt lims apipe-bridge commands
Remove old `gmt vcf somatic-variation-to-vcf`.

It refers to a non-existent snp130.txt and is mostly a wrapper for other
gmt commands.
Remove old and deprecated `gmt somatic strand-filter`.

It refers to an executable with "test" in the name in a home directory.
dont pull back instrument data when the AnP is on hold
set the labels to the object properties rather than the id ones
Add "id" properties for object-based inputs for use in config
Temporarily add "add_*" methods for indirect input accessors

We will be modifying UR to handle this case correctly, but this is
a stopgap until then
get rid of now unused properties
Remove half-baked `gmt simulation generate-reads`.
Remove examples that point to a home directory.
Update tophat2 to set itself in /etc/alternatives
add instrumentation to file-based lock/unlock
add more instrumentation to file-based lock/unlock
only check allocation owner_class_name if it got an allocation

This could maybe do more in the case that the allocation doesn't exist
but for now at least keep it from crashing.
looks like a new input named allosome_names was added to builds
Updated class browser cache.
Updated `genome` tab completion.
Updated `gmt` tab completion.
Remove duplicated comment with command-line.

(Cleaning up references to home directories.)