refactor: strip prose comments from code; rationale lives in docs

Code files carry no comments beyond shebangs, directives and one-line
pointers to docs/pipeline_notes.md. The facts the comments held (tool
quirks, thresholds, ordering constraints, container build choices) were
moved into the notes under the module they belong to, and README now
documents the rescue and threshold-policy parameters and the three
project parameter sets. No code token changed.

Co-Authored-By: Claude Fable 5.1 <[email protected]>