Reorganize paperspec commands and pin dependency versions (#2)

Reviewed-on: #2

.gitignore

@@ -3,7 +3,10 @@ __pycache__/
 *.db
 *.db.assets/
 
-# the website, built by tools/site.py
+# the package version, written by setuptools-scm when the package is built or installed
+/src/paperspec/_version.py
+
+# the website, built by `paperspec site`
 /_site/
 
 # pixi environments
@@ -758,7 +761,7 @@ FodyWeavers.xsd
 
 # End of https://www.toptal.com/developers/gitignore/api/osx,python,pycharm,windows,visualstudio,visualstudiocode,zsh,jetbrains,jupyternotebooks
 
-# The Visual Studio rules above ignore every packages/ and log/ folder; these hold fixtures that tools/check.py
+# The Visual Studio rules above ignore every packages/ and log/ folder; these hold fixtures that `paperspec check`
 # compares byte for byte, so keep them.
 !/fixtures/packages/*
 !/fixtures/records/log/