docs: move rationale to pipeline_notes, drop non-English comments

Restores the convention this repository already documents: the long rationale lives
in docs/pipeline_notes.md and the code keeps at most a one-line pointer to the
relevant anchor. Recent edits for the letizia_mouse, nicotine_hippo and microbiota
projects had regressed to long inline prose, in Portuguese.

Moved to docs/pipeline_notes.md:
  - index_reference: the mt_contig gate, why optional:true is safe for the existing
    projects, and why a project with its own reference needs its own directory.
  - basecall: why the unclassified publishDir does not cause the duplication the
    other one would, why it is off by default, why containsKey is used instead of
    the elvis operator, and why per-barcode outputs carry an ${id}_ prefix.
  - new "Project parameters" section documenting every non-obvious key of
    parameters/microbiota/.

Also translates the INDEX_REFERENCE runtime message to English. No behavioral change.