diff -r ac0bbc1e5d79 -r 88e01c8f013e metatools/sysdeftools/lib/mergesysdef-module.xsl
--- a/metatools/sysdeftools/lib/mergesysdef-module.xsl	Mon Sep 13 13:11:19 2010 +0800
+++ b/metatools/sysdeftools/lib/mergesysdef-module.xsl	Mon Sep 13 13:52:18 2010 +0100
@@ -213,7 +213,6 @@
 			<xsl:with-param name="replaces" select="$replaces"/>
 		</xsl:apply-templates>
 
-
 		<!-- tack on any remaining layers -->
 		<xsl:apply-templates mode="merge-copy-of" select="$other/systemModel/layer[not(@before) and not(following-sibling::*[@id=current()/layer/@id]) and not(@id=current()/layer/@id)]">
 			<xsl:with-param name="origin" select="$down"/>
@@ -273,67 +272,16 @@
 	<xsl:choose>
 		<xsl:when test="not($to-sort)"/>  <!-- nothing left to copy. stop -->
 		<xsl:when test="not($base)"/>  <!-- reached end. stop -->
-		<xsl:when test="$base[1]/@id=$end/following-sibling::*[1]/@id"/> <!-- passed $end. Stop -->
-		<xsl:when test="$base[1]/@id = $to-sort[1]/@id">  <!-- both lists start with same item -->
-			<xsl:if test="$base[1]/@id!=$end/@id"> <!-- not at end, so keep going -->
-				<xsl:call-template name="copy-sorted-content">
-					<xsl:with-param name="base" select="$base[position() != 1]"/>
-					<xsl:with-param name="to-sort" select="$to-sort[position() != 1]"/>
-					<xsl:with-param name="remainder" select="$remainder"/>
-					<xsl:with-param name="start" select="$start"/>
-					<xsl:with-param name="end" select="$end"/>
-					<xsl:with-param name="down" select="$down"/>
-				</xsl:call-template>		
-			</xsl:if>
-		</xsl:when>	
-		<xsl:when test="$remainder[@id = $base[1]/@id]"> <!-- left over item is in $base -->
-			<xsl:call-template name="copy-sorted-content">
-				<xsl:with-param name="base" select="$base[position() != 1]"/>
-				<xsl:with-param name="to-sort" select="$to-sort"/>
-				<xsl:with-param name="remainder" select="$remainder[@id != $base[1]/@id]"/>
-				<xsl:with-param name="start" select="$start"/>
-				<xsl:with-param name="end" select="$end"/>
-				<xsl:with-param name="down" select="$down"/>
-			</xsl:call-template>		
-		</xsl:when>
-		<xsl:when test="not($base[@id = $to-sort[1]/@id])"> <!-- in to-sort, but not base -->		
-			<xsl:if test="$base[1]/@id=$end/@id  and not($base[@id=$to-sort[1]/@before])">
-			 	<!-- if at end, then this needs to be copied
-					don't copy if the before ID is found in $base	-->
-				<xsl:apply-templates mode="merge-copy-of" select="$to-sort[1]">
-					<xsl:with-param name="origin" select="$down"/>
-					<xsl:with-param name="root" select="$end/ancestor::SystemDefinition"/>
-				</xsl:apply-templates>
-			</xsl:if>			
-		<xsl:call-template name="copy-sorted-content">
-			<xsl:with-param name="base" select="$base"/>
-			<xsl:with-param name="to-sort" select="$to-sort[position() != 1]"/>
-			<xsl:with-param name="remainder" select="$remainder"/>
-			<xsl:with-param name="start" select="$start"/>
-			<xsl:with-param name="end" select="$end"/>
-			<xsl:with-param name="down" select="$down"/>
-		</xsl:call-template>		
-		</xsl:when>	
-		<xsl:when test="not($to-sort[@id = $base[1]/@id])"> <!-- in base, but not to-sort -->		
-		<xsl:call-template name="copy-sorted-content">
-			<xsl:with-param name="base" select="$base[position() != 1]"/>
-			<xsl:with-param name="to-sort" select="$to-sort"/>
-			<xsl:with-param name="remainder" select="$remainder"/>
-			<xsl:with-param name="start" select="$start"/>
-			<xsl:with-param name="end" select="$end"/>
-			<xsl:with-param name="down" select="$down"/>
-		</xsl:call-template>		
-		</xsl:when>	
-		<xsl:when test="$base[@id = $to-sort[1]/@id]"> <!-- is in base, but not 1st one-->
-			<xsl:call-template name="copy-sorted-content">
-				<xsl:with-param name="base" select="$base"/>
-				<xsl:with-param name="to-sort" select="$to-sort[position() != 1] "/>
-				<xsl:with-param name="remainder" select="$remainder | $to-sort[1]"/>
-				<xsl:with-param name="start" select="$start"/>
-				<xsl:with-param name="end" select="$end"/>
-				<xsl:with-param name="down" select="$down"/>
-			</xsl:call-template>
-		</xsl:when>	
+		<xsl:otherwise>
+			<xsl:for-each select="$to-sort">
+				<xsl:if test="((@before=$end/@id) or not(@before) or not($base/ancestor::SystemDefinition//*[@id=current()/@before])) and not($base[@id=current()/@id])">
+					<xsl:apply-templates mode="merge-copy-of" select=".">
+						<xsl:with-param name="origin" select="$down"/>
+						<xsl:with-param name="root" select="$end/ancestor::SystemDefinition"/>
+					</xsl:apply-templates>
+				</xsl:if>
+			</xsl:for-each>
+		</xsl:otherwise>	
 	</xsl:choose>
 </xsl:template>
 
@@ -374,6 +322,22 @@
 </xsl:template>
 
 
+<xsl:template name="best-prev"><xsl:param name="cur" select="."/><xsl:param name="alt"/>
+<xsl:if test="$alt">
+<xsl:variable name="prev" select="$cur/preceding-sibling::*[@id][1]"/> 
+<xsl:choose>
+	<xsl:when test="not($prev)"/>
+	<xsl:when test="$alt/preceding-sibling::*[@id=$prev/@id]"><xsl:value-of select="$prev/@id"/></xsl:when>
+	<xsl:otherwise>
+		<xsl:call-template name="best-prev">
+			<xsl:with-param name="cur" select="$prev"/>
+			<xsl:with-param name="alt" select="$alt"/>
+		</xsl:call-template>
+	</xsl:otherwise>
+</xsl:choose>
+</xsl:if>
+</xsl:template>
+
 <xsl:template match="layer | package | collection | component" mode="merge-models">
 	<xsl:param name="other"/>	<!-- the downstream item of the parent's rank that contains a potential items this is merged with -->
 	<xsl:param name="up"/>
@@ -386,9 +350,9 @@
 	<xsl:choose>
 		<xsl:when test="$replaces[.=$this/@id] or (self::component and $match)">  <!-- replace the item instead of merge -->
 			<xsl:message>Note: <xsl:value-of select="name()"/> "<xsl:value-of select="@id"/>" in "<xsl:value-of select="../@id"/>" <xsl:choose>
-				<xsl:when test="self::component and $match">overridden in downstream sysdef</xsl:when>
-				<xsl:otherwise><xsl:for-each select="$replaces[.=$this/@id]/..">replaced by <xsl:value-of select="name()"/> "<xsl:value-of select="@id"/>" in "<xsl:value-of select="../@id"/>"</xsl:for-each></xsl:otherwise>
-			</xsl:choose>
+					<xsl:when test="self::component and $match">overridden in downstream sysdef</xsl:when>
+					<xsl:otherwise><xsl:for-each select="$replaces[.=$this/@id]/..">replaced by <xsl:value-of select="name()"/> "<xsl:value-of select="@id"/>" in "<xsl:value-of select="../@id"/>"</xsl:for-each></xsl:otherwise>
+				</xsl:choose>
 			</xsl:message>
 			<!-- if the removed item is in the downstream doc, just copy that and ignore the upstream contents -->
 			<xsl:apply-templates mode="merge-copy-of" select="$match">
@@ -400,29 +364,37 @@
 		<xsl:otherwise>
 			<!-- remove this if it's in the list of stuff to be replaced-->
 
+<xsl:variable name="prev-id">
+	<xsl:call-template name="best-prev">
+		<xsl:with-param name="alt" select="$match"/>
+	</xsl:call-template>
+</xsl:variable>
+
 	<!-- prev = the previous item before the current one (no metas, only named items)-->
-	<xsl:variable name="prev" select="preceding-sibling::*[@id][1]"/> 
+	<xsl:variable name="prev" select="preceding-sibling::*[@id=$prev-id]"/> 
 
-	<!-- copy all items between this and prev  that are solely in the downstream model -->	 		
+
+	<!-- copy all items between this and prev that are solely in the downstream model -->	 		
 
 	<xsl:choose>
-		<xsl:when test="$match and (not($prev) or $other/*[@id= $prev/@id] )">
+		<xsl:when test="$match and $prev">
 			<xsl:call-template name="copy-sorted-content">
 				<xsl:with-param name="base" select="../*[@id]"/>
-				<xsl:with-param name="to-sort" select="$other/*[@id]"/>
+				<xsl:with-param name="to-sort" select="$other/*[@id][following-sibling::*[@id=$match/@id]][preceding-sibling::*[@id=$prev/@id]]"/>
 				<xsl:with-param name="start" select="$prev"/>
 				<xsl:with-param name="end" select="."/>
 				<xsl:with-param name="down" select="$down"/>
 			</xsl:call-template>
 		</xsl:when>
-	<xsl:when test="not($match/preceding-sibling::*[@id=$this/../*/@id]) and $other/*[@id= current()/@id]/preceding-sibling::*[@id and not(@before)]">
-		<!-- if this is the first item in other that's also in this, then put all new items from other here -->
-		<xsl:apply-templates mode="merge-copy-of" select="$match/preceding-sibling::*[@id and not(@before)]">
-			<xsl:with-param name="origin" select="$down"/>
-			<xsl:with-param name="root" select="$this/ancestor::SystemDefinition"/>	
-			<xsl:with-param name="replaces" select="$replaces"/>
-		</xsl:apply-templates>
-	</xsl:when>
+		<xsl:when test="$match and not($prev)">
+			<xsl:call-template name="copy-sorted-content">
+				<xsl:with-param name="base" select="../*[@id]"/>
+				<xsl:with-param name="to-sort" select="$other/*[@id][following-sibling::*[@id=$match/@id]]"/>
+				<xsl:with-param name="start" select="$prev"/>
+				<xsl:with-param name="end" select="."/>
+				<xsl:with-param name="down" select="$down"/>
+			</xsl:call-template>
+		</xsl:when>
 	</xsl:choose>
 
  	<!-- just copy anything identified as being before this, assume they're all ok -->
@@ -432,7 +404,6 @@
 		<xsl:with-param name="root" select="$this/ancestor::SystemDefinition"/>	
 		<xsl:with-param name="replaces" select="$replaces"/>
 	</xsl:apply-templates>
-
 	
 	<xsl:copy>
 		<xsl:apply-templates select="@*" mode="merge-models"> <!-- copy upstream attributes -->