Add an `--alternative_assembly` flag

[j23414]

Clarify how to combine primary and alternative assemblies for arrow, purgedups, and freebayes.

primary                                                                purgedups (primary?)
               > cat (with different headers) -> arrow -> (separate) <
alternative                                                                 ....  \_combine with alt -> purgedups?

[j23414]

Step 1 is primary + alt -> ARROW (without falcon unzip) -> SPLIT -> purge_dups and then manual scaffolding step Step 2 is scaf_primary + alt + mito -> ARROW + merfin -> FREEBAYES -> FREEBAYES -> SPLIT

[j23414]

fixed in purge_dups branch, will merge when all checks pass