halExtract --root makes corrupt output

[glennhickey]

This was raised here: ComparativeGenomicsToolkit/cactus#933

And it's easy enough to reproduce

halExtract evolverMammals.hal --root Anc1 Anc1.hal --inMemory
hal2maf Anc1.hal Anc1.maf --inMemory
<segfault>

The file can be repaired with another extract (!)

halExtract Anc1.hal Anc1.fix.hal --inMemory
hal2maf Anc1.fix.hal Anc1.maf --inMemory
<works!>

So the --root cutting option of halExtract must be forgetting to update a link somehwere.