docs: move remaining prose comments into pipeline_notes

Applies one criterion across src/ and parameters/: a run of two or more consecutive
comment lines is prose that restates docs/pipeline_notes.md, so it moves out; a lone
comment line sitting at the exact statement it protects is code knowledge, so it stays.

Every fact removed was verified to already exist in docs/pipeline_notes.md before
deletion. The one exception was src/bin/validate_haplogroup_f6.sh, whose header block
held the only copy of the script's purpose and usage; that content is now a new
"validate_haplogroup_f6" section in the docs, and the header is gone from the script.

What survives in the code is the set of one-line regression guards, e.g. "do NOT add
--header to pileup: it space-delimits cols >10 and breaks tabix/dmr", each still
carrying its docs anchor. These are kept deliberately: the warning is only useful at
the line where someone would otherwise reintroduce the bug.

No behavioral change.