The following patch(pasted below and also attached as an attachment) fixes
the bug that \setupFLOWlines[rulethickness=whatever] have no effects:
--- m-chart.lua.orig    2013-03-12 09:22:42.000000000 +0800
+++ m-chart.lua 2013-08-15 10:52:08.617268698 +0800
@@ -499,7 +499,7 @@
                     local linesettings = settings.line
                     context("flow_shape_line_color := \\MPcolor{%s} ;",
linesettings.color)
                     context("flow_shape_fill_color := \\MPcolor{%s} ;",
linesettings.backgroundcolor)
-                    context("flow_shape_line_width := %s ; ",
points(linesettingsrulethickness))
+                    context("flow_shape_line_width := %s ; ",
points(linesettings.rulethickness))
                 elseif focus[cell.focus] or focus[cell.name] then
                     local focussettings = settings.focus
                     context("flow_shape_line_color := \\MPcolor{%s} ;",
focussettings.framecolor)
@@ -580,7 +580,7 @@
                             context("flow_touchshape := %s ;",
linesettings.offset == v_none and "true" or "false")
                             context("flow_dsp_x := %s ; flow_dsp_y := %s
;",connection.dx or 0, connection.dy or 0)
                             context("flow_connection_line_color :=
\\MPcolor{%s} ;",linesettings.color)
-                            context("flow_connection_line_width := 2pt
;",points(linesettings.rulethickness))
+                            context("flow_connection_line_width := %s
;",points(linesettings.rulethickness))
                             context("flow_connect_%s_%s (%s) (%s,%s,%s)
(%s,%s,%s)
;",where_cell,where_other,j,cellx,celly,what_cell,otherx,othery,what_other)
                             context("flow_dsp_x := 0 ; flow_dsp_y := 0 ;")
                         end