Reorganize paperspec commands and pin dependency versions (#2)

Reviewed-on: #2

registry/README.md

@@ -43,7 +43,7 @@ A rule's meaning never changes, and a retired rule's ID is never reused, so tool
 A tool can match on the `rule` field, whose meaning is looked up in `rules.json`, and treat the message as text for people.
 [Chapter 22, section 22.4](../spec/22-conformance.md#224-rules) lists the ID prefixes.
 Each directory in `fixtures/invalid/` has an `expect.json` that names the rule it breaks.
-The reference checker (`tools/check.py`) fails if that rule is not in `rules.json`.
+The reference checker (`paperspec check`) fails if that rule is not in `rules.json`.
 
 ## Adding stamp rules