And here are the patches..

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diff -r 8bb4ca7fba40 runtime/doc/options.txt
--- a/runtime/doc/options.txt	Wed Oct 22 22:09:01 2014 +0200
+++ b/runtime/doc/options.txt	Thu Oct 30 07:52:39 2014 +0100
@@ -3853,17 +3853,16 @@
 
 						*'highlight'* *'hl'*
 'highlight' 'hl'	string	(default (as a single string):
-				     "8:SpecialKey,@:NonText,d:Directory,
-				     e:ErrorMsg,i:IncSearch,l:Search,m:MoreMsg,
-				     M:ModeMsg,n:LineNr,N:CursorLineNr,
-				     r:Question,s:StatusLine,S:StatusLineNC,
-				     c:VertSplit, t:Title,v:Visual,
-				     w:WarningMsg,W:WildMenu,
-				     f:Folded,F:FoldColumn,A:DiffAdd,
-				     C:DiffChange,D:DiffDelete,T:DiffText,
-				     >:SignColumn,B:SpellBad,P:SpellCap,
-				     R:SpellRare,L:SpellLocal,-:Conceal,
-				     +:Pmenu,=:PmenuSel,
+				     "8:SpecialKey,~:EndOfBuffer,@:NonText,
+				     d:Directory,e:ErrorMsg,i:IncSearch,
+				     l:Search,m:MoreMsg,M:ModeMsg,n:LineNr,
+				     N:CursorLineNr,r:Question,s:StatusLine,
+				     S:StatusLineNC,c:VertSplit,t:Title,
+				     v:Visual,w:WarningMsg,W:WildMenu,f:Folded,
+				     F:FoldColumn,A:DiffAdd,C:DiffChange,
+				     D:DiffDelete,T:DiffText,>:SignColumn,
+				     B:SpellBad,P:SpellCap,R:SpellRare,
+				     L:SpellLocal,-:Conceal,+:Pmenu,=:PmenuSel,
 				     x:PmenuSbar,X:PmenuThumb")
 			global
 			{not in Vi}
@@ -3872,6 +3871,7 @@
 	first character in a pair gives the occasion, the second the mode to
 	use for that occasion.  The occasions are:
 	|hl-SpecialKey|	 8  Meta and special keys listed with ":map"
+	|hl-EndOfBuffer|	~  lines after the last line in the buffer
 	|hl-NonText|	 @  '~' and '@' at the end of the window and
 			    characters from 'showbreak'
 	|hl-Directory|	 d  directories in CTRL-D listing and other special
diff -r 8bb4ca7fba40 runtime/doc/syntax.txt
--- a/runtime/doc/syntax.txt	Wed Oct 22 22:09:01 2014 +0200
+++ b/runtime/doc/syntax.txt	Thu Oct 30 07:52:39 2014 +0100
@@ -4761,6 +4761,7 @@
 DiffDelete	diff mode: Deleted line |diff.txt|
 							*hl-DiffText*
 DiffText	diff mode: Changed text within a changed line |diff.txt|
+							*hl-EndofBuffer*
 							*hl-ErrorMsg*
 ErrorMsg	error messages on the command line
 							*hl-VertSplit*
@@ -4789,10 +4790,10 @@
 							*hl-MoreMsg*
 MoreMsg		|more-prompt|
 							*hl-NonText*
-NonText		'~' and '@' at the end of the window, characters from
-		'showbreak' and other characters that do not really exist in
-		the text (e.g., ">" displayed when a double-wide character
-		doesn't fit at the end of the line).
+NonText		'@' at the end of the window, characters from 'showbreak'
+		and other characters that do not really exist in the text
+		(e.g., ">" displayed when a double-wide character doesn't
+		fit at the end of the line).
 							*hl-Normal*
 Normal		normal text
 							*hl-Pmenu*
diff -r 8bb4ca7fba40 runtime/syntax/vim.vim
--- a/runtime/syntax/vim.vim	Wed Oct 22 22:09:01 2014 +0200
+++ b/runtime/syntax/vim.vim	Thu Oct 30 07:52:39 2014 +0100
@@ -68,7 +68,7 @@
 syn keyword vimGroup contained	Comment Constant String Character Number Boolean Float Identifier Function Statement Conditional Repeat Label Operator Keyword Exception PreProc Include Define Macro PreCondit Type StorageClass Structure Typedef Special SpecialChar Tag Delimiter SpecialComment Debug Underlined Ignore Error Todo 
 
 " Default highlighting groups {{{2
-syn keyword vimHLGroup contained	ColorColumn Cursor CursorColumn CursorIM CursorLine CursorLineNr DiffAdd DiffChange DiffDelete DiffText Directory ErrorMsg FoldColumn Folded IncSearch LineNr MatchParen Menu ModeMsg MoreMsg NonText Normal Pmenu PmenuSbar PmenuSel PmenuThumb Question Scrollbar Search SignColumn SpecialKey SpellBad SpellCap SpellLocal SpellRare StatusLine StatusLineNC TabLine TabLineFill TabLineSel Title Tooltip VertSplit Visual VisualNOS WarningMsg WildMenu 
+syn keyword vimHLGroup contained	ColorColumn Cursor CursorColumn CursorIM CursorLine CursorLineNr DiffAdd DiffChange DiffDelete DiffText Directory EndOfBuffer ErrorMsg FoldColumn Folded IncSearch LineNr MatchParen Menu ModeMsg MoreMsg NonText Normal Pmenu PmenuSbar PmenuSel PmenuThumb Question Scrollbar Search SignColumn SpecialKey SpellBad SpellCap SpellLocal SpellRare StatusLine StatusLineNC TabLine TabLineFill TabLineSel Title Tooltip VertSplit Visual VisualNOS WarningMsg WildMenu 
 syn match vimHLGroup contained	"Conceal"
 syn case match
 
diff -r 8bb4ca7fba40 src/option.c
--- a/src/option.c	Wed Oct 22 22:09:01 2014 +0200
+++ b/src/option.c	Thu Oct 30 07:52:39 2014 +0100
@@ -469,7 +469,7 @@
 #if defined(FEAT_DIFF) || defined(FEAT_FOLDING) || defined(FEAT_SPELL) \
 	|| defined(FEAT_VERTSPLIT) || defined(FEAT_CLIPBOARD) \
 	|| defined(FEAT_INS_EXPAND) || defined(FEAT_SYN_HL) || defined(FEAT_CONCEAL)
-# define HIGHLIGHT_INIT "8:SpecialKey,@:NonText,d:Directory,e:ErrorMsg,i:IncSearch,l:Search,m:MoreMsg,M:ModeMsg,n:LineNr,N:CursorLineNr,r:Question,s:StatusLine,S:StatusLineNC,c:VertSplit,t:Title,v:Visual,V:VisualNOS,w:WarningMsg,W:WildMenu,f:Folded,F:FoldColumn,A:DiffAdd,C:DiffChange,D:DiffDelete,T:DiffText,>:SignColumn,-:Conceal,B:SpellBad,P:SpellCap,R:SpellRare,L:SpellLocal,+:Pmenu,=:PmenuSel,x:PmenuSbar,X:PmenuThumb,*:TabLine,#:TabLineSel,_:TabLineFill,!:CursorColumn,.:CursorLine,o:ColorColumn"
+# define HIGHLIGHT_INIT "8:SpecialKey,~:EndOfBuffer,@:NonText,d:Directory,e:ErrorMsg,i:IncSearch,l:Search,m:MoreMsg,M:ModeMsg,n:LineNr,N:CursorLineNr,r:Question,s:StatusLine,S:StatusLineNC,c:VertSplit,t:Title,v:Visual,V:VisualNOS,w:WarningMsg,W:WildMenu,f:Folded,F:FoldColumn,A:DiffAdd,C:DiffChange,D:DiffDelete,T:DiffText,>:SignColumn,-:Conceal,B:SpellBad,P:SpellCap,R:SpellRare,L:SpellLocal,+:Pmenu,=:PmenuSel,x:PmenuSbar,X:PmenuThumb,*:TabLine,#:TabLineSel,_:TabLineFill,!:CursorColumn,.:CursorLine,o:ColorColumn"
 #else
 # define HIGHLIGHT_INIT "8:SpecialKey,@:NonText,d:Directory,e:ErrorMsg,i:IncSearch,l:Search,m:MoreMsg,M:ModeMsg,n:LineNr,N:CursorLineNr,r:Question,s:StatusLine,S:StatusLineNC,t:Title,v:Visual,w:WarningMsg,W:WildMenu,>:SignColumn,*:TabLine,#:TabLineSel,_:TabLineFill"
 #endif
diff -r 8bb4ca7fba40 src/screen.c
--- a/src/screen.c	Wed Oct 22 22:09:01 2014 +0200
+++ b/src/screen.c	Thu Oct 30 07:52:39 2014 +0100
@@ -2151,7 +2151,7 @@
 
 	/* make sure the rest of the screen is blank */
 	/* put '~'s on rows that aren't part of the file. */
-	win_draw_end(wp, '~', ' ', row, wp->w_height, HLF_AT);
+	win_draw_end(wp, '~', ' ', row, wp->w_height, HLF_EOB);
     }
 
     /* Reset the type of redrawing required, the window has been updated. */
diff -r 8bb4ca7fba40 src/syntax.c
--- a/src/syntax.c	Wed Oct 22 22:09:01 2014 +0200
+++ b/src/syntax.c	Thu Oct 30 07:52:39 2014 +0100
@@ -6744,6 +6744,8 @@
 #endif
 static char *(highlight_init_both[]) =
     {
+	CENT("EndOfBuffer term=bold ctermfg=Blue",
+	     "EndOfBuffer term=bold ctermfg=Blue gui=bold guifg=Blue"),
 	CENT("ErrorMsg term=standout ctermbg=DarkRed ctermfg=White",
 	     "ErrorMsg term=standout ctermbg=DarkRed ctermfg=White guibg=Red guifg=White"),
 	CENT("IncSearch term=reverse cterm=reverse",
diff -r 8bb4ca7fba40 src/vim.h
--- a/src/vim.h	Wed Oct 22 22:09:01 2014 +0200
+++ b/src/vim.h	Thu Oct 30 07:52:39 2014 +0100
@@ -1342,6 +1342,7 @@
 {
     HLF_8 = 0	    /* Meta & special keys listed with ":map", text that is
 		       displayed different from what it is */
+    , HLF_EOB	    /* after the last line in the buffer */
     , HLF_AT	    /* @ and ~ characters at end of screen, characters that
 		       don't really exist in the text */
     , HLF_D	    /* directories in CTRL-D listing */
@@ -1389,7 +1390,7 @@
 
 /* The HL_FLAGS must be in the same order as the HLF_ enums!
  * When changing this also adjust the default for 'highlight'. */
-#define HL_FLAGS {'8', '@', 'd', 'e', 'h', 'i', 'l', 'm', 'M', \
+#define HL_FLAGS {'8', '~', '@', 'd', 'e', 'h', 'i', 'l', 'm', 'M', \
 		  'n', 'N', 'r', 's', 'S', 'c', 't', 'v', 'V', 'w', 'W', \
 		  'f', 'F', 'A', 'C', 'D', 'T', '-', '>', \
 		  'B', 'P', 'R', 'L', \
diff -r 2259e704c58c runtime/colors/blue.vim
--- a/runtime/colors/blue.vim	Thu Oct 30 13:59:51 2014 +0100
+++ b/runtime/colors/blue.vim	Thu Oct 30 14:06:10 2014 +0100
@@ -53,3 +53,4 @@
 hi FoldColumn	guibg=gray30		guifg=black	ctermbg=gray		ctermfg=black
 hi cIf0			guifg=gray			ctermfg=gray
 
+hi link EndOfBuffer NonText
diff -r 2259e704c58c runtime/colors/darkblue.vim
--- a/runtime/colors/darkblue.vim	Thu Oct 30 13:59:51 2014 +0100
+++ b/runtime/colors/darkblue.vim	Thu Oct 30 14:06:10 2014 +0100
@@ -64,3 +64,5 @@
 hi PmenuSel guifg=#c0c0c0 guibg=#2050d0
 hi PmenuSbar guifg=blue guibg=darkgray
 hi PmenuThumb guifg=#c0c0c0
+
+hi link EndOfBuffer NonText
diff -r 2259e704c58c runtime/colors/delek.vim
--- a/runtime/colors/delek.vim	Thu Oct 30 13:59:51 2014 +0100
+++ b/runtime/colors/delek.vim	Thu Oct 30 14:06:10 2014 +0100
@@ -52,4 +52,6 @@
 hi Statement  cterm=bold ctermfg=Blue	     gui=bold guifg=blue
 hi Type	      cterm=NONE ctermfg=Blue	     gui=bold guifg=blue
 
+hi link EndOfBuffer NonText
+
 " vim: sw=2
diff -r 2259e704c58c runtime/colors/desert.vim
--- a/runtime/colors/desert.vim	Thu Oct 30 13:59:51 2014 +0100
+++ b/runtime/colors/desert.vim	Thu Oct 30 14:06:10 2014 +0100
@@ -104,5 +104,6 @@
 hi Ignore	ctermfg=darkgrey
 hi Error	cterm=bold ctermfg=7 ctermbg=1
 
+hi link EndOfBuffer NonText
 
 "vim: sw=4
diff -r 2259e704c58c runtime/colors/evening.vim
--- a/runtime/colors/evening.vim	Thu Oct 30 13:59:51 2014 +0100
+++ b/runtime/colors/evening.vim	Thu Oct 30 14:06:10 2014 +0100
@@ -53,4 +53,6 @@
 endif
 hi Ignore ctermfg=DarkGrey guifg=grey20
 
+hi link EndOfBuffer NonText
+
 " vim: sw=2
diff -r 2259e704c58c runtime/colors/koehler.vim
--- a/runtime/colors/koehler.vim	Thu Oct 30 13:59:51 2014 +0100
+++ b/runtime/colors/koehler.vim	Thu Oct 30 14:06:10 2014 +0100
@@ -70,3 +70,4 @@
 hi link Delimiter		Special
 hi link SpecialComment	Special
 hi link Debug			Special
+hi link EndOfBuffer		NonText
diff -r 2259e704c58c runtime/colors/morning.vim
--- a/runtime/colors/morning.vim	Thu Oct 30 13:59:51 2014 +0100
+++ b/runtime/colors/morning.vim	Thu Oct 30 14:06:10 2014 +0100
@@ -53,4 +53,6 @@
 endif
 hi Ignore ctermfg=LightGrey guifg=grey90
 
+hi link EndOfBuffer NonText
+
 " vim: sw=2
diff -r 2259e704c58c runtime/colors/murphy.vim
--- a/runtime/colors/murphy.vim	Thu Oct 30 13:59:51 2014 +0100
+++ b/runtime/colors/murphy.vim	Thu Oct 30 14:06:10 2014 +0100
@@ -39,3 +39,5 @@
 hi Title		term=bold	   ctermfg=LightMagenta gui=bold	guifg=Pink
 hi WarningMsg	term=standout  ctermfg=LightRed   guifg=Red
 hi Visual		term=reverse   cterm=reverse	  gui=NONE		guifg=white guibg=darkgreen
+
+hi link EndOfBuffer NonText
diff -r 2259e704c58c runtime/colors/peachpuff.vim
--- a/runtime/colors/peachpuff.vim	Thu Oct 30 13:59:51 2014 +0100
+++ b/runtime/colors/peachpuff.vim	Thu Oct 30 14:06:10 2014 +0100
@@ -58,3 +58,4 @@
 hi Error term=reverse cterm=bold ctermfg=7 ctermbg=1 gui=bold guifg=White guibg=Red
 hi Todo term=standout ctermfg=0 ctermbg=3 guifg=Blue guibg=Yellow
 
+hi link EndOfBuffer NonText
diff -r 2259e704c58c runtime/colors/ron.vim
--- a/runtime/colors/ron.vim	Thu Oct 30 13:59:51 2014 +0100
+++ b/runtime/colors/ron.vim	Thu Oct 30 14:06:10 2014 +0100
@@ -43,3 +43,5 @@
 hi FoldColumn	guibg=gray30 guifg=white
 hi cIf0			guifg=gray
 hi diffOnly	guifg=red gui=bold
+
+hi link EndOfBuffer NonText
diff -r 2259e704c58c runtime/colors/shine.vim
--- a/runtime/colors/shine.vim	Thu Oct 30 13:59:51 2014 +0100
+++ b/runtime/colors/shine.vim	Thu Oct 30 14:06:10 2014 +0100
@@ -57,4 +57,6 @@
 endif
 hi Ignore ctermfg=LightGrey guifg=grey90
 
+hi link EndOfBuffer NonText
+
 " vim: sw=2
diff -r 2259e704c58c runtime/colors/slate.vim
--- a/runtime/colors/slate.vim	Thu Oct 30 13:59:51 2014 +0100
+++ b/runtime/colors/slate.vim	Thu Oct 30 14:06:10 2014 +0100
@@ -54,3 +54,5 @@
 :hi Underlined cterm=underline ctermfg=5
 :hi Error guifg=White guibg=Red cterm=bold ctermfg=7 ctermbg=1
 :hi SpellErrors guifg=White guibg=Red cterm=bold ctermfg=7 ctermbg=1
+
+:hi link EndOfBuffer NonText

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