Sunbeam extensions should use builtin dependency handling

[louiejtaylor]

Title. Also many of them could benefit from a README update. Am working through these at my own leisure; anyone is welcome to help out if they feel like it!

Extensions:

• [x] sbx_template
• [x] sbx_subsample
• [x] sbx_metaphlan (done, outstanding issues)
• [x] sbx_coassembly (outstanding issues)
• [ ] sbx_kaiju (open issues and PRs)
• [x] sbx_anvio
• [x] sbx_spades
• ~~sbx_shortbred~~ (tricky install--this one should likely be re-written to use vsearch)
• [ ] sbx_gene_clusters (requires manual database download, but I think it's still convertible)
• [x] sbx_select_contigs
• [x] sbx_rgi
• [x] sbx_eggnog
• [x] sbx_dedup
• [x] sbx_kraken_uniq
• [x] sbx_krakenhll (should we retire this one in favor of the krakenuniq version?)

These are most of the ones from https://www.sunbeam-labs.org/directory.html (and I think ones people might use). I don't think it's necessary to update the examples from the paper.