I've noticed a minor glitch with the fossil diff --by command in conjunction with CR+LF line endings, i.e. it looks like CR+LF may "inject" additional lines in some cases:

• Screenshots: fossil diff --by vs. Fossil web UI diff

Left snippet (must be saved with CR+LF line endings):

set "__CLEAN=0"
set "__CLEANRC=0"
set "__BUILD=1"

:parse_args
if /I "%~1" == "clean" (
  set "__CLEAN=1"
  if not "%__BUILD%" == "2" set "__BUILD=0"
  shift /1
  goto :parse_args
)
if /I "%~1" == "cleanrc" (
  set "__CLEANRC=1"
  if not "%__BUILD%" == "2" set "__BUILD=0"
  shift /1
  goto :parse_args
)
if /I "%~1" == "build" (
  set "__BUILD=2"
  shift /1
  goto :parse_args
)

Right snippet (must be saved with CR+LF line endings):

set "__BUILD=1"
set "__CLEAN=0"

:parse_args
if /I "%~1" == "build" (
  set "__BUILD=2"
  shift /1
  goto :parse_args
)
if /I "%~1" == "clean" (
  set "__CLEAN=2"
  if not "%__BUILD%" == "2" set "__BUILD=0"
  shift /1
  goto :parse_args
)
if /I "%~1" == "cleanrc" (
  if not "%__CLEAN%" == "2" set "__CLEAN=1"
  if not "%__BUILD%" == "2" set "__BUILD=0"
  shift /1
  goto :parse_args
)