Reorganize paperspec commands and pin dependency versions (#2)

Reviewed-on: #2

sql/README.md

@@ -31,7 +31,7 @@ dolt sql < sql/doc.sql && dolt sql < sql/store.sql
 The PostgreSQL database `lab` and the Dolt repository must already exist.
 The `sqlite3` line runs as shown; the `psql` and `dolt` lines follow the portability rules of [chapter 13](../spec/13-database.md#131-portability) but have not been run on those engines in this repository.
 
-To load packages into SQLite without pixi, run `python3 tools/load.py --sqlite lab.db PACKAGE…` with Python 3.14 and two packages, `jsonschema` and `cryptography` installed.
+To load packages into SQLite without pixi, install the package with its `tools` extra on Python 3.14, then run `paperspec load --sqlite lab.db PACKAGE…`.
 The file [docs/examples.md](../docs/examples.md#load-packages-into-sqlite) has queries to try.
 The loader copies files that have no table (assets, dataset files, derived files) by SHA-256 into `lab.db.assets/`.
 
@@ -57,7 +57,8 @@ On `fixtures/packages/hale2026harmonic-damb` it returns one row, `hca6dc5`: the
 - Names: no table, column or index name is reserved in SQLite, PostgreSQL or MySQL (Dolt is MySQL-compatible).
   The formats' `key`, `index`, `at`, `by`, `before` and `after` become `doc_key`, `idx`, `made_at`, `signer`, `before_hash` and `after_hash`.
 - Round trip: each row keeps every property of its record, so unloading restores the same bytes and the same manifest hash.
-  Unloading copies the files with no table from the asset store, which must travel with the database. `tools/check.py` tests this for every fixture package.
+  Unloading copies the files with no table from the asset store, which must travel with the database.
+  `paperspec check` tests this for every fixture package.
 - Derived tables: `citations`, `receipt_nodes` and `annotation_targets` are built on load for queries and are not part of the package.
 
 ## Status