Add note that files in InitialWorkDir must have path in output directory.

Author: Peter Amstutz

v1.0/CommandLineTool.yml

@@ -789,6 +789,13 @@ $graph:
         May be an expression.  If so, the expression return value must validate
         as `{type: array, items: [File, Directory]}`.
 
+        Files or Directories which are listed in the input parameters and
+        appear in the `InitialWorkDirRequirement` listing must have their
+        `path` set to their staged location in the designated output directory.
+        If the same File or Directory appears more than once in the
+        `InitialWorkDirRequirement` listing, the implementation must choose
+        exactly one value for `path`; how this value is chosen is undefined.
+
 
 - name: EnvVarRequirement
   type: record

v1.1.0-dev1/CommandLineTool.yml

@@ -840,6 +840,13 @@ $graph:
         May be an expression.  If so, the expression return value must validate
         as `{type: array, items: [File, Directory]}`.
 
+        Files or Directories which are listed in the input parameters and
+        appear in the `InitialWorkDirRequirement` listing must have their
+        `path` set to their staged location in the designated output directory.
+        If the same File or Directory appears more than once in the
+        `InitialWorkDirRequirement` listing, the implementation must choose
+        exactly one value for `path`; how this value is chosen is undefined.
+
 
 - name: EnvVarRequirement
   type: record