Reorganize paperspec commands and pin dependency versions (#2)

Reviewed-on: #2

docs/examples.md

@@ -9,7 +9,7 @@ The formats are version 0.1.0, and each is `candidate` or `provisional` in `regi
 
 Run every command from the root of the repository, <https://git.scient.ing/infra/paperspec>.
 With [pixi](https://pixi.sh), `pixi run <task>` sets up the environment first.
-Every command also works without pixi, with Python 3.14 and two packages, `jsonschema` and `cryptography` installed and standard command-line tools (the `sed` command in the last section is the GNU version of `sed`).
+Every command also works without pixi once the checkout is installed with `pip install -e ".[tools]"` on Python 3.14, given standard command-line tools (the `sed` command in the last section is the GNU version of `sed`).
 
 ## Run the checks
 
@@ -19,10 +19,10 @@ This shows how to confirm that the repository's specification, fixtures and test
 pixi run check
 ```
 
-`pixi run check` lints the Markdown, then runs `python tools/check.py`, the repository's reference checker.
+`pixi run check` lints the Markdown, then runs `paperspec check`, the repository's reference checker.
 Each section prints how many checks it ran, and the last line is `All checks pass.`
-`pixi run quick`, or `python3 tools/check.py --quick`, skips the slowest part, which rebuilds everything and compares it byte for byte.
-Without pixi, the Markdown lint is a separate step (`markdownlint-cli2`); `tools/check.py` does not run it.
+`pixi run quick`, or `paperspec check --quick`, skips the slowest part, which rebuilds everything and compares it byte for byte.
+Without pixi, the Markdown lint is a separate step (`markdownlint-cli2`); `paperspec check` does not run it.
 
 ## Recompute a hash by hand
 
@@ -146,7 +146,7 @@ This shows that the same packages can live in a database and be queried with SQL
 pixi run load --sqlite lab.db fixtures/packages/hale2026harmonic-damb fixtures/packages/okafor2025solvent-acth fixtures/packages/writer2027fixed-ynr7.v3
 ```
 
-Without pixi, run `python3 tools/load.py` with the same arguments.
+Without pixi, run `paperspec load` with the same arguments.
 
 ```text
 hale2026harmonic-damb: 75 nodes
@@ -154,7 +154,7 @@ okafor2025solvent-acth: 15 nodes
 writer2027fixed-ynr7.v3: 15 nodes
 ```
 
-The tables are those of [sql/doc.sql](../sql/doc.sql) and [sql/store.sql](../sql/store.sql), which run unchanged on Dolt and PostgreSQL as well ([chapter 13](../spec/13-database.md)); `tools/check.py` exercises them on SQLite only, and this repository has not yet run them on Dolt or PostgreSQL.
+The tables are those of [sql/doc.sql](../sql/doc.sql) and [sql/store.sql](../sql/store.sql), which run unchanged on Dolt and PostgreSQL as well ([chapter 13](../spec/13-database.md)); `paperspec check` exercises them on SQLite only, and this repository has not yet run them on Dolt or PostgreSQL.
 Here are four queries, in Python's `sqlite3` so that nothing else is needed.
 
 ```python