Clarify secondaryFiles behaviour (#6)

* Clarify secondaryFiles behavior

In the previous reading of the specification, it is unclear whether setting the secondaryFiles in inputs/outputs must affect the secondaryFiles attribute of primary files and therefore make the secondaryFiles attribute travel with the primary files.

Author: ThomasHickman

CommandLineTool.yml

@@ -70,8 +70,9 @@ $graph:
         * Clarify semantics of `shellQuote`
         * Expressions are now allowed to evaluate to `null` or `Dirent` in
           [InitialWorkDirRequirement.listing](#InitialWorkDirRequirement).
+        * Clarify behavior of secondaryFiles on output.
         * [Addition](#Requirements_and_hints) of `cwl:requirements` field to
-          input object documents
+          input object documents.
         * Clarify behavior of `glob` for absolute paths and symlinks.
         * Clarify behavior of `glob` to include directories.
 

Process.yml

@@ -467,9 +467,11 @@ $graph:
         Only valid when `type: File` or is an array of `items: File`.
 
         Provides a pattern or expression specifying files or directories that
-        must be included alongside the primary file.  All listed secondary
-        files must be present.  An implementation may fail workflow execution
-        if an expected secondary file does not exist.
+        must be included alongside the primary file. An implementation must append 
+        these files/directories to the `secondaryFiles` property of the primary file.
+        These files/directories must be transferred alongside the primary file.
+        An implementation may fail workflow execution if an expected secondary file
+        does not exist.
 
         If the value is an expression, the value of `self` in the expression
         must be the primary input or output File object to which this binding