Reorganize paperspec commands and pin dependency versions (#2)

Reviewed-on: #2

context/README.md

@@ -96,11 +96,12 @@ Three of the nine fixture annotations have only an `AnchorSelector` (the section
 - Reader: Follow [chapter 6](../spec/06-anchors.md) to resolve an anchor.
   The file `vectors/resolve.jsonl` resolves seventeen anchors against `fixtures/packages/hale2026harmonic-damb` and gives every outcome.
 - JSON-LD processor: Use a JSON-LD 1.1 processor; the context relies on `@json` and `@version` 1.1.
-- Checker: `schemas/annotation.schema.json` and `schemas/layer.schema.json` validate the files. `tools/check.py` also checks that each annotation's ID derives from its content and that the receipt at `fixtures/records/layer/receipt.json` covers each `confirmed` annotation.
+- Checker: `schemas/annotation.schema.json` and `schemas/layer.schema.json` validate the files.
+  `paperspec check` also checks that each annotation's ID derives from its content and that the receipt at `fixtures/records/layer/receipt.json` covers each `confirmed` annotation.
 
 The traps:
 
-- No test vector pins the context, and nothing in `tools/` reads `scienting-1.jsonld`.
+- No test vector pins the context, and nothing here runs a JSON-LD processor on it; `paperspec check` and `paperspec site` read only its term IRIs.
   The schemas require only that `@context` be an array of at least two non-empty strings; they do not check the URLs.
   A file with a wrong context can pass the checker and still expand wrongly.
 - `@context` is part of an annotation's content hash (the hash covers everything except `status`, `receipt` and `modified`).