Reorganize paperspec commands and pin dependency versions (#2)

Reviewed-on: #2

CONTRIBUTING.md

@@ -13,11 +13,11 @@ The schemas, SQL, registries, vectors and fixtures then follow the chapter ([spe
 2. **Change the schemas, SQL and registries** that the rule shapes.
    A new refusal gets a rule ID in [registry/rules.json](registry/rules.json).
 3. **Compute, never type, the expected values.**
-   Change the oracle in [tools/oracle/](tools/oracle/) to apply the rule, and add the case that shows it to [tools/build.py](tools/build.py): a vector, a fixture or a broken package in `fixtures/invalid/`.
+   Change the oracle in [src/paperspec/](src/paperspec/) to apply the rule, and add the case that shows it to [src/paperspec/cli/build.py](src/paperspec/cli/build.py): a vector, a fixture or a broken package in `fixtures/invalid/`.
    Then run `pixi run build`, which rewrites `fixtures/` and `vectors/`.
 4. **Run the checks.**
    `pixi run check` must end with `All checks pass.`
-   Without pixi, run `python3 tools/check.py`, with Python 3.14 and two packages, `jsonschema` and `cryptography` installed.
+   Without pixi, install the checkout with `pip install -e ".[tools]"` on Python 3.14, then run `paperspec check`.
 5. **Record the change** in [CHANGELOG.md](CHANGELOG.md).
 
 ## Versions
@@ -29,17 +29,20 @@ A rebuild that changes any file under `vectors/` or any hash in `fixtures/` is a
 ## New node kinds and run kinds
 
 Propose a kind with the vector or fixture that shows it.
-A node kind needs its row in [chapter 3](spec/03-nodes.md), the node schema, and its entry in the `CHILDREN` table of `tools/oracle/model.py`.
+A node kind needs its row in [chapter 3](spec/03-nodes.md), the node schema, and its entry in the `CHILDREN` table of `src/paperspec/model.py`.
 A run kind needs its row in [section 3.5](spec/03-nodes.md#35-inline-runs) and the node schema, and its text in the plain projection ([3.6](spec/03-nodes.md#36-the-plain-projection)) and in the strict and lossy projections ([5.3](spec/05-hashes.md#53-the-strict-projection), [5.5](spec/05-hashes.md#55-the-lossy-projection)).
 
 ## Releasing
 
-A release is a tag on `main` whose version is the top heading of [CHANGELOG.md](CHANGELOG.md).
+A release is a tag `vX.Y.Z` on `main`, and its version is the version of the Python package `paperspec`, which setuptools-scm reads from the tag.
+A release that changes the formats takes the new format version, which becomes the top heading of [CHANGELOG.md](CHANGELOG.md) and the version that `pixi.toml` and the registries state.
+A release that changes only the code takes the next patch version and records it as a subsection under the current format version, as `### 0.1.1` sits under `## 0.1.0`.
+Pushing the tag publishes the package to the Gitea package registry ([deploy/](deploy/README.md#publish-the-python-package)).
 Before tagging:
 
 1. `pixi run check` passes on Linux and macOS, which the workflow in `.gitea/workflows/` runs on every push.
-   The check also confirms that every count the prose states (formats, schemas, vectors, broken packages) matches the repository, and that `pixi.toml`, the registries and `tools/build.py` state the same version.
-2. `python3 tools/stress.py` passes with its default seed, and with one or two others.
+   The check also confirms that every count the prose states (formats, schemas, vectors, broken packages) matches the repository, and that `pixi.toml`, the registries and `src/paperspec/cli/build.py` state the same version.
+2. `paperspec stress` passes with its default seed, and with one or two others.
 3. The website is published from the release ([deploy/](deploy/README.md)), and the JSON-LD context at `https://paperspec.scient.ing/context/scienting-1.jsonld` and a schema at its `$id` both answer with their media types.
    Layers claim to be W3C Web Annotations, and a JSON-LD processor that cannot fetch the context cannot read them.
 4. The decisions that freeze on release are made: enumeration values and format identifiers never change meaning afterwards ([spec/22 §22.5](spec/22-conformance.md#225-stability)), so a name worth changing is changed now.
@@ -56,4 +59,4 @@ The keys in `fixtures/keys/` are public test keys and must never sign anything e
 
 ## Licenses
 
-Each path keeps the license that [LICENSE.md](LICENSE.md) gives it: prose CC-BY-4.0, the normative data CC0-1.0, and `tools/` Apache-2.0.
+Each path keeps the license that [LICENSE.md](LICENSE.md) gives it: prose CC-BY-4.0, the normative data CC0-1.0, and the code in `src/` and `tools/` Apache-2.0.