FIX: Backport minimal RTD config fixes so v0.13.0 builds on RTD

The v0.13.0 release tag predates every RTD fix that landed on main
(#1673, #1676, #1682, #1740, #1745, #1793, #1825), so RTD couldn't
build v0.13.0 from the tag and the `stable` alias was stuck.

This commit backports only the two surgical changes needed to make
the v0.13.0 content build under the current RTD environment, with
zero changes to any documentation content. After this lands, RTD's
v0.13.0 version is reconfigured to track this branch rather than
the immutable tag.

1. .readthedocs.yaml -- the tag's config had two issues that combined
   to make RTD fail before producing any output:
     * build.jobs.build.commands is not a valid key (RTD only accepts
       html/pdf/epub/htmlzip under build.jobs.build). This was a hard
       config-validation error that aborted the build before pip
       install ran.
     * jupyter-book build --all builds frontmatter exports only (PDF
       per doc/myst.yml), not the static HTML site. --html is required
       to produce _build/html/index.html, which is what RTD serves.
   The fix merges the commands into the html block, adds --html, and
   corrects the cp source to _build/html/. The legacy python.install
   block is kept because v0.13.0 uses [project.optional-dependencies]
   rather than PEP 735 [dependency-groups] (the latter was introduced
   on main after the tag).

2. doc/myst.yml -- removes two TOC entries that never resolved:
     * api/pyrit_setup_initializers.md -- gen_api_md.py does not emit
       this page because pyrit.setup has its own API members and the
       script only expands pure-aggregate modules.
     * api/pyrit_ui.md -- pyrit/ui/ never existed in the v0.13.0 tree.
   Both would surface as 'Table of contents entry does not exist'
   errors during the build.

The strict-mode, cross-reference, and TOC-validation fixes from PRs
#1745 and #1793 are not needed at v0.13.0 because the v0.13.0 build
does not use --strict and does not invoke the TOC validator.

Verified locally: pip install .[dev] + the pre_build steps + the
build step produce doc/_build/html/index.html (196 KB) and 1850
site files.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: romanlutz

.readthedocs.yaml

@@ -16,10 +16,14 @@ build:
       - python build_scripts/gen_api_md.py
     build:
       html:
-        - cd doc && jupyter-book build --all
-      commands:
+        # --all builds frontmatter exports (PDF, per doc/myst.yml); --html is
+        # required to produce the static HTML site (_build/html/index.html)
+        # that RTD serves. The 3 commands previously sat in a separate
+        # `commands:` block, which is not a valid `build.jobs.build` key in
+        # RTD and caused config validation to fail before any commands ran.
+        - cd doc && jupyter-book build --all --html
         - mkdir -p $READTHEDOCS_OUTPUT/html
-        - cp -r doc/_build/site/* $READTHEDOCS_OUTPUT/html/
+        - cp -r doc/_build/html/* $READTHEDOCS_OUTPUT/html/
 
 python:
    install:

doc/myst.yml

@@ -196,10 +196,7 @@ project:
         - file: api/pyrit_scenario.md
         - file: api/pyrit_score.md
         - file: api/pyrit_setup.md
-          children:
-            - file: api/pyrit_setup_initializers.md
         - file: api/pyrit_show_versions.md
-        - file: api/pyrit_ui.md
     - file: blog/README.md
       children:
         - file: blog/2025_06_06.md