Update language around files and direcotories being read only. Closes #…

…495.

CHANGELOG.md

@@ -89,6 +89,8 @@ version 1.2.0
 
 + Added `Directory` type.
 
++ Added clarification that input files and directories should be treated as read-only.
+
 version 1.1.1
 ---------------------------
 

SPEC.md

@@ -3543,6 +3543,28 @@ task call_variants_safe {
 }
 ```
 
+Runtime engines **should** treat input `File`s and `Directory`s as read-only, e.g., by setting their permissions appropriately on the local file system, or by localizing them to a directory marked as read-only.
+
+Note starting in WDL 2.0 engines **must** treat input `File`s and `Directory`s as read-only.
+
+A common pattern for tasks that require multiple input files to be in the same directory is to create a new directory in the execution environment and soft-link the files into that directory.
+
+```wdl
+task two_files_one_directory {
+  input {
+    File bam
+    File bai
+  }
+  String prefix = basename(bam, ".bam")
+  command <<<
+  mkdir inputs
+  ln -s ~{bam} inputs/~{prefix}.bam
+  ln -s ~{bai} inputs/~{prefix}.bam.bai
+  varcall inputs/~{prefix}.bam
+  >>>
+}
+```
+
 ##### Special Case: Versioning Filesystem
 
 Two or more versions of a file in a versioning filesystem might have the same name and come from the same directory. In that case, the following special procedure must be used to avoid collision: