Update SoftwareRequirement spec based on codefest discussion.

Author: Peter Amstutz

v1.0/CommandLineTool.yml

@@ -647,46 +647,50 @@ $graph:
   name: SoftwareRequirement
   extends: "#ProcessRequirement"
   doc: |
-    Software that should be configured in the environment of the defined
-    process.
-
-    While absolute portability between platforms can be achieved with container
-    technologies like Docker, this mechanism provides an inexact and imprecise
-    fallback. The inexact nature is due to this standard not specifying the
-    base operating environment of the process or how the that environment is to
-    be configured as a result of these hints. The imprecise nature of these
-    hints is due to the `name` and `version` fields being unstructured and not
-    namespaced. The optional `identifier` field is recommended so that users
-    and platforms can distinguish between software that has the same name.
+    A list of software packages that should be configured in the environment of
+    the defined process.
   fields:
     - name: "class"
       type: "string"
       doc: "Always 'SoftwareRequirement'"
       jsonldPredicate:
         "_id": "@type"
         "_type": "@vocab"
-    - name: spec
+    - name: packages
       type:
         type: array
-        items: SoftwareSpec
+        items: SoftwarePackage
       doc: "The list of software to be configured."
+      jsonldPredicate:
+        mapSubject: name
+        mapPredicate: specs
 
-- name: SoftwareSpec
+- name: SoftwarePackage
   type: record
   fields:
     - name: name
       type: string
-      doc: "The name of the software to be configured."
+      doc: "The common name of the software to be configured."
       jsonldPredicate: "@id"
     - name: "version"
-      type: string?
+      type: string[]?
       doc: "The (optional) version of the software to configured."
-    - name: "identifier"
-      type: string?
+    - name: specs
+      type: string[]?
       doc: |
-        The (optional) identifier of the software to be configured. Should be a
-        IRI such as an [RRID](http://www.identifiers.org/rrid/SCR_001156).
-        Example: `http://identifiers.org/rrid/RRID:SCR_001156`
+        Must be one or more IRIs identifying resources for installing or
+        enabling the software.  Implementations may provide resolvers which map
+        well-known software spec IRIs to some configuration action.
+
+        For example, an IRI `https://packages.debian.org/jessie/bowtie` could
+        be resolved with `apt-get install bowtie`.  An IRI
+        `https://anaconda.org/bioconda/bowtie` could be resolved with `conda
+        install -c bioconda bowtie`.
+
+        Tools may also provide IRIs to index entries such as
+        [RRID](http://www.identifiers.org/rrid/), such as
+        `http://identifiers.org/rrid/RRID:SCR_005476`
+
 
 - name: Dirent
   type: record