diff --git a/pom.xml b/pom.xml
index 52406ed..6d8b628 100644
--- a/pom.xml
+++ b/pom.xml
@@ -56,6 +56,12 @@
             <version>2.0.14</version>
         </dependency>
 
+        <dependency>
+            <groupId>net.sf.saxon</groupId>
+            <artifactId>Saxon-HE</artifactId>
+            <version>9.5.1-2</version>
+        </dependency>
+
         <dependency>
             <groupId>com.rackspace.papi.components</groupId>
             <artifactId>translation</artifactId>
@@ -64,15 +70,8 @@
 
         <dependency>
             <groupId>com.xmlcalabash</groupId>
-            <artifactId>calabash</artifactId>
-            <version>0.9.38</version>
-	    <!-- <version>1.0.2-94</version> -->
-        </dependency>
-
-        <dependency>
-            <groupId>net.sf.saxon</groupId>
-            <artifactId>saxon-ee</artifactId>
-            <version>9.4.0.6</version>
+            <artifactId>xmlcalabash</artifactId>
+            <version>1.0.13-94</version>
         </dependency>
 
         <dependency>
diff --git a/src/main/java/com/rackspace/cloud/api/docs/pipeline/CalabashPipelineBuilder.java b/src/main/java/com/rackspace/cloud/api/docs/pipeline/CalabashPipelineBuilder.java
index bb8b550..73ee7c7 100644
--- a/src/main/java/com/rackspace/cloud/api/docs/pipeline/CalabashPipelineBuilder.java
+++ b/src/main/java/com/rackspace/cloud/api/docs/pipeline/CalabashPipelineBuilder.java
@@ -6,6 +6,7 @@ import com.xmlcalabash.core.XProcConfiguration;
 import com.xmlcalabash.core.XProcMessageListener;
 import com.xmlcalabash.core.XProcRuntime;
 import com.xmlcalabash.runtime.XPipeline;
+import com.xmlcalabash.util.Input;
 import com.xmlcalabash.util.XProcURIResolver;
 import net.sf.saxon.s9api.SaxonApiException;
 
@@ -47,7 +48,7 @@ public class CalabashPipelineBuilder implements PipelineBuilder {
          InputStreamUriParameterResolver resolver = new InputStreamUriParameterResolver(new XProcURIResolver(runtime));
          resolver.addResolver(new ClassPathUriResolver());
          runtime.setURIResolver(resolver);
-         XPipeline pipeline = runtime.load(pipelineUri);
+         XPipeline pipeline = runtime.load(new Input(pipelineUri));
          return new CalabashPipeline(pipeline, runtime, resolver, legacySourceOutput);
       } catch (SaxonApiException ex) {
          // TODO: Should we log the exception here?
@@ -66,7 +67,7 @@ public class CalabashPipelineBuilder implements PipelineBuilder {
             streamResolver.addResolver(resolver);
          }
          runtime.setURIResolver(streamResolver);
-         XPipeline pipeline = runtime.load(pipelineUri);
+         XPipeline pipeline = runtime.load(new Input(pipelineUri));
          return new CalabashPipeline(pipeline, runtime, streamResolver);
       } catch (SaxonApiException ex) {
          // TODO: Should we log the exception here?
diff --git a/src/main/resources/etc/pipeline-library.xml b/src/main/resources/etc/pipeline-library.xml
index 66d7c21..b160a69 100644
--- a/src/main/resources/etc/pipeline-library.xml
+++ b/src/main/resources/etc/pipeline-library.xml
@@ -332,7 +332,7 @@
       <p:output port="result" sequence="true"/>
    </p:declare-step>
    <p:declare-step type="p:xsl-formatter" xml:id="xsl-formatter">
-      <p:input port="source"/>
+      <p:input port="source" primary="true"/>
       <p:input port="parameters" kind="parameter"/>
       <p:output port="result" primary="false"/>
       <p:option name="href" required="true" cx:type="xsd:anyURI"/>
diff --git a/src/main/resources/pdf.xpl b/src/main/resources/pdf.xpl
index 49c4dfc..a0a281f 100644
--- a/src/main/resources/pdf.xpl
+++ b/src/main/resources/pdf.xpl
@@ -9,7 +9,7 @@
   <p:import href="classpath:///rackspace-library.xpl"/><!-- classpath:/// -->
   <p:import href="http://xmlcalabash.com/extension/steps/library-1.0.xpl"/>
 
-  <p:input port="source"/>
+  <p:input port="source" primary="true"/>
   <p:output port="result"/>
 
   <p:input port="parameters" kind="parameter"/>
diff --git a/src/main/resources/rackspace-library.xpl b/src/main/resources/rackspace-library.xpl
index 1d35568..5ae052b 100644
--- a/src/main/resources/rackspace-library.xpl
+++ b/src/main/resources/rackspace-library.xpl
@@ -16,7 +16,7 @@
         type="l:validate-transform-idrefs"
         name="main">
         
-        <p:input port="source" /> <!--sequence="false" primary="true"-->
+        <p:input port="source" primary="true"/> <!--sequence="false" primary="true"-->
         <p:input port="schema" sequence="true" >
             <p:document  href="classpath:///rng/rackbook.rng"/> 
         </p:input>
@@ -169,7 +169,7 @@ setting failOnValidationError to no in your pom.
         type="l:validate-transform"
         name="main">
         
-        <p:input port="source" /> 
+        <p:input port="source" primary="true" /> 
         <p:input port="schema" sequence="true" >
             <p:document  href="classpath:///rng/rackbook.rng"/> 
         </p:input>
@@ -496,7 +496,7 @@ setting failOnValidationError to no in your pom.
         version="1.0"
         name="extensions-info-step">
         
-        <p:input port="source"/>
+        <p:input port="source" primary="true"/>
         
         <p:output port="secondary" primary="false" sequence="true"/>
         <p:output port="result" primary="true" >
@@ -540,7 +540,7 @@ setting failOnValidationError to no in your pom.
             * Test with api.openstack.org xpl
         -->
 
-        <p:input port="source"/>
+        <p:input port="source" primary="true"/>
 
         <p:output port="result" primary="true">
             <p:pipe step="group" port="result"/>
@@ -799,7 +799,7 @@ setting failOnValidationError to no in your pom.
         version="1.0"
         name="process-embedded-wadl-step">
         
-        <p:input port="source"/>
+        <p:input port="source" primary="true"/>
         
         <p:output port="result" primary="true">
             <p:pipe step="process-embedded-wadl-xslt-3" port="result"/>
@@ -918,7 +918,7 @@ setting failOnValidationError to no in your pom.
         version="1.0"
         name="docbook-xslt2-preprocess-step">
         
-        <p:input port="source"/>
+        <p:input port="source" primary="true"/>
         
         <p:output port="result" primary="true">
             <p:pipe step="group" port="result"/>
@@ -974,7 +974,7 @@ setting failOnValidationError to no in your pom.
         version="1.0"
         name="process-embedded-wadl-step-war">
         
-        <p:input port="source"/>
+        <p:input port="source" primary="true"/>
         
         <p:output port="result" primary="true">
             <p:pipe step="process-embedded-wadl-xslt" port="result"/>
@@ -1006,7 +1006,7 @@ setting failOnValidationError to no in your pom.
         version="1.0"
         name="add-stop-chunking-pis-step">
         
-        <p:input port="source"/>
+        <p:input port="source" primary="true"/>
         
         <p:output port="result" primary="true">
             <p:pipe step="add-stop-chunking-pis-xslt" port="result"/>
@@ -1038,7 +1038,7 @@ setting failOnValidationError to no in your pom.
         version="1.0"
         name="bookinfo-step">
         
-        <p:input port="source"/>
+        <p:input port="source" primary="true"/>
         
         <p:output port="secondary" primary="false" sequence="true"/>
         
@@ -1465,7 +1465,7 @@ setting failOnValidationError to no in your pom.
             that we use the root element's xml:id as the current doc
             id. </p:documentation>
 
-        <p:input port="source"/>
+        <p:input port="source" primary="true"/>
 
         <p:output port="result" primary="true">
             <p:pipe step="normalize-olinks-xslt" port="result"/>
diff --git a/src/main/resources/test-error.xpl b/src/main/resources/test-error.xpl
index 3fd6fbf..f6f7499 100644
--- a/src/main/resources/test-error.xpl
+++ b/src/main/resources/test-error.xpl
@@ -3,7 +3,7 @@
   xmlns:p="http://www.w3.org/ns/xproc"
   name="main">
   
-  <p:input port="source" /> <!--sequence="false" primary="true"-->
+  <p:input port="source" primary="true"/> <!--sequence="false" primary="true"-->
   <p:input port="schema" sequence="true" >
     <p:document  href="http://docs-beta.rackspace.com/oxygen/13.1/mac/author/frameworks/rackbook/5.0/rng/rackbook.rng"/> <!--http://docs-beta.rackspace.com/oxygen/13.1/mac/author/frameworks/rackbook/5.0/-->
   </p:input>
diff --git a/src/main/resources/validate-transform.xpl b/src/main/resources/validate-transform.xpl
index e149e83..bb2b466 100644
--- a/src/main/resources/validate-transform.xpl
+++ b/src/main/resources/validate-transform.xpl
@@ -5,7 +5,7 @@
   type="l:validate-transform"
   name="main">
   
-  <p:input port="source" /> <!--sequence="false" primary="true"-->
+  <p:input port="source" primary="true"/> <!--sequence="false" primary="true"-->
   <p:input port="schema" sequence="true" >
     <p:document  href="classpath:///rng/rackbook.rng"/> <!--http://docs-beta.rackspace.com/oxygen/13.1/mac/author/frameworks/rackbook/5.0/-->
   </p:input>
diff --git a/src/main/resources/wadl2html.xpl b/src/main/resources/wadl2html.xpl
index 8335b4b..64c128d 100644
--- a/src/main/resources/wadl2html.xpl
+++ b/src/main/resources/wadl2html.xpl
@@ -7,7 +7,7 @@
   xmlns:cx="http://xmlcalabash.com/ns/extensions"
   name="main">
   
-  <p:input port="source"/> 
+  <p:input port="source" primary="true"/> 
   <p:input port="parameters" kind="parameter"/>
   <p:output port="result"/>
 
diff --git a/src/main/resources/war.xpl b/src/main/resources/war.xpl
index f2d4a97..cc8f2be 100644
--- a/src/main/resources/war.xpl
+++ b/src/main/resources/war.xpl
@@ -6,7 +6,7 @@
   xmlns:cx="http://xmlcalabash.com/ns/extensions"
   name="main">
   
-  <p:input port="source"/> 
+  <p:input port="source" primary="true"/> 
   <p:input port="parameters" kind="parameter"/>
   <p:output port="result"/>
 
diff --git a/src/main/resources/webhelp.xpl b/src/main/resources/webhelp.xpl
index 3eac1de..3fc10a5 100644
--- a/src/main/resources/webhelp.xpl
+++ b/src/main/resources/webhelp.xpl
@@ -4,7 +4,7 @@
   xmlns:l="http://xproc.org/library"
   xmlns:cx="http://xmlcalabash.com/ns/extensions" name="main">
 
-  <p:input port="source"/>
+  <p:input port="source" primary="true"/>
   <p:input port="parameters" kind="parameter"/>
   <p:output port="result"/>