Remove reference files now maintained in food-dbs

[dksuperdock]

Removes the reference files from reference/ now that they live in food-dbs, and moves the non-reference files out of that folder.

• Deletes reference/references/ (trnL and 12Sv5 reference FASTAs) and reference/sql-creation/ (taxonomizr SQL scripts). Current references are in food-dbs data/outputs/dada2-compatible/.
• Deletes reference/common-names/. These CSVs move to food-dbs in Add common names CSVs moved from mb-pipeline food-dbs#8.
• Moves reference/anonymizer/ to anonymizer/, and TEMPLATE_samplesheet.csv and sampledata.csv to templates/. File contents are unchanged.
• Updates the reference FASTA links in pipeline/README.md and Pipeline-to-Phyloseq.Rmd to point to food-dbs, and updates the README structure tree.

Merge after LAD-LAB/food-dbs#8 so the common names CSVs stay available.

After this merges, the handbook's anonymizer page needs its paths changed from reference/anonymizer to anonymizer.