snapshot: working tree state at the end of the microbiota run (2026-07-23)

WARNING: this commit is a SUPERPOSITION, not a clean single-project state.
The tree was never committed between 2026-06-14 (f17684d4) and this snapshot,
so it accumulates edits from three different projects, identifiable by mtime:

  2026-06-24  sub_workflows/BASECALLING.nf                          letizia_mouse
  2026-07-03  main.nf, modules/{calculate_coverage,modkit,mtdna_metrics}.nf,
              nextflow.config, sub_workflows/MODKIT_AND_MULTIQC.nf   nicotine_hippo
  2026-07-23  modules/{basecall,index_reference}.nf                  microbiota

The branch name reflects the LAST project that ran on this tree, which is the
only one this state is faithful to. The letizia_mouse (24-25 Jun 2026) and
nicotine_hippo (3 Jul 2026) states must be reconstructed from the Nextflow
cache, which was exported to text in the same operation.

Also adds parameters/{letizia_mouse,nicotine_hippo,microbiota}/, which were
untracked because they had never been added, not because of .gitignore.