Amazing.

"A bird I call my little Yorkla Harlin" clinches it.

My educated guess is that the later stanzas about disease, a man in blue, and prison arose in university, prison, or military circles, presumably in the 20th century, when bawdy songs became a lot bawdier - or so it seems.

The "prison cell" stanza, however, parodies George F. Root's once famous Civil War song about a POW, "Tramp, Tramp, Tramp" (1863), which begins:

"In the prison cell I sit,
Thinking, mother dear, of you."