--- a/make/common/ProcessMarkdown.gmk	Mon Nov 26 14:18:32 2018 +0100
+++ b/make/common/ProcessMarkdown.gmk	Mon Nov 26 18:50:55 2018 +0100
@@ -30,11 +30,12 @@
 
 # Helper function for SetupProcessMarkdown
 # $1: The $1 from SetupProcessMarkdown
-# $2: The name of the current source file, relative to $1_SRC
+# $2: The name of the current source file, relative to the dir given in $3
+# $3: The directory of the current source file
 define ProcessMarkdown
   $1_$2_OUTPUT_FILE := $$($1_DEST)/$$(basename $2)$$($1_FILE_EXT)
   $1_$2_TARGET_DIR := $$(dir $$($1_$2_OUTPUT_FILE))
-  $1_$2_INPUT_FILE := $$($1_SRC)/$2
+  $1_$2_INPUT_FILE := $3/$2
   $1_$2_MARKER := $$(subst /,_,$1_$2)
 
   ifneq ($$($1_REPLACEMENTS), )
@@ -64,7 +65,7 @@
     endif
   endif
 
-  $1_$2_OPTIONS := $$(shell $$(GREP) _pandoc-options_: $$($1_SRC)/$2 | $$(CUT) -d : -f 2-)
+  $1_$2_OPTIONS := $$(shell $$(GREP) _pandoc-options_: $3/$2 | $$(CUT) -d : -f 2-)
 
   ifneq ($$($1_FILTER), )
     $1_$2_OPTIONS += --filter $$($1_FILTER)
@@ -111,10 +112,10 @@
 # and the targets generated are listed in a variable by that name.
 #
 # Remaining parameters are named arguments. These include:
-#   SRC      : Source root dir (defaults to dir of first file)
-#   DEST     : Dest root dir
+#   DEST     : Destination root dir
 #   FILES    : List of files to copy with absolute paths, or path relative to SRC.
-#              Must be in SRC.
+#   SRC      : Source root dir; if given keep input files hierarchy relative to
+#              SRC in DEST, otherwise flatten structure into DEST.
 #   FORMAT   : The target format (defaults to html5)
 #   FILE_EXT : The file extension to replace .md with (defaults to .html)
 #   OPTIONS  : Additional options to pandoc
@@ -133,11 +134,6 @@
     $$(error DEST is missing in SetupProcessMarkdown $1)
   endif
 
-  # Default SRC to the dir of the first file.
-  ifeq ($$($1_SRC), )
-    $1_SRC := $$(dir $$(firstword $$($1_FILES)))
-  endif
-
   # If no target format is specified, default to html5.
   ifeq ($$($1_FORMAT), )
     $1_FORMAT := html5
@@ -158,11 +154,23 @@
     endif
   endif
 
-  # Remove any trailing slash from SRC and DEST
-  $1_SRC := $$(patsubst %/,%,$$($1_SRC))
+  # Remove any trailing slash
   $1_DEST := $$(patsubst %/,%,$$($1_DEST))
 
-  $$(foreach f, $$(patsubst $$($1_SRC)/%,%,$$($1_FILES)), \
-    $$(eval $$(call ProcessMarkdown,$1,$$f)) \
-  )
+  ifeq ($$($1_SRC), )
+    # No SRC given, assume we're flattening all files into output dir.
+    $$(foreach f, $$($1_FILES), \
+      $$(eval $$(call ProcessMarkdown,$1,$$(notdir $$f),$$(patsubst %/,%,$$(dir $$f)))) \
+    )
+  else
+    # Remove any trailing slash
+    $1_SRC := $$(patsubst %/,%,$$($1_SRC))
+
+    $$(foreach f, $$(patsubst $$($1_SRC)/%,%,$$($1_FILES)), \
+      $$(eval $$(call ProcessMarkdown,$1,$$f,$$($1_SRC))) \
+    )
+  endif
+
+
+
 endef