Reorganize paperspec commands and pin dependency versions (#2)

Reviewed-on: #2

vectors/README.md

@@ -73,19 +73,19 @@ Some files change the procedure:
   Compute the field for each listed case and compare across the group.
 - `fingerprints.jsonl` needs the download-stamp rules in [registry/stamps/scienting-stamps-1.json](../registry/stamps/scienting-stamps-1.json), which each case names in `rules`.
 - `resolve.jsonl`, `grading.jsonl` and `targets.jsonl` name a package by a path from the repository root.
-  All three use `fixtures/packages/hale2026harmonic`.
+  All three use `fixtures/packages/hale2026harmonic-damb`.
 
 Several files also mix more than one kind of case, told apart by their fields.
 `ids.jsonl` has minting cases and letter-first cases, `keyed.jsonl` and `signatures.jsonl` have a case for each derivation or record, `spotcheck.jsonl` has sample-size cases and one full sample, and `rights.jsonl` has stage checks (a `stage` field), backend checks (a `backend` field) and one combining case (neither).
 
-The reference checker in [tools/](../tools/README.md) runs all twenty-five files, together with the rest of the repository's checks:
+The reference checker, `paperspec check` ([tools/](../tools/README.md)), runs all twenty-five files, together with the rest of the repository's checks:
 
 ```sh
-python3 tools/check.py --quick
+paperspec check --quick
 ```
 
-It needs Python 3.14 and two packages, `jsonschema` and `cryptography`, and has no option to run one file.
-It tests the reference implementation in `tools/oracle/` against the vectors.
+It runs in a checkout, through pixi (`pixi run quick`) or after `pip install -e ".[tools]"` on Python 3.14, and has no option to run one file.
+It tests the reference implementation in `src/paperspec/` against the vectors.
 It does not test yours.
 
 ## What each file tests
@@ -136,7 +136,7 @@ The specification, and the vectors with it, are at version 0.1.0 ([0.3](../spec/
 The specification has 32 formats: 19 are `candidate` and 13 are `provisional` in [registry/formats.json](../registry/formats.json).
 A candidate format changes only with a recorded reason and a new or changed vector ([22.5](../spec/22-conformance.md#225-stability)).
 
-A passing run shows one thing: for these inputs, your implementation computes the same values as the reference implementation in `tools/oracle/`.
+A passing run shows one thing: for these inputs, your implementation computes the same values as the reference implementation in `src/paperspec/`.
 That code computed the expected outputs, and `pixi run build` regenerates them ([tools/](../tools/README.md)).
 The vectors hold 311 cases in all, some of them small: `hashes.jsonl` has one document, `alignment.jsonl` one pair of readings, `offsets.jsonl` two cases.