Python API reference: correct and complete it for cldk 2.0.0 #14

The Python API reference (reference/python-api/) needs a pass for cldk 2.0.0. An audit ran every sample against cldk==2.0.0 from PyPI on the docs' sample projects (Flask, Commons CLI 1.7.0, Zod). Separate verifier agents then checked every finding.

Authored text (outside the generated block):

• Dead links: /cocoa/ and /guides/common-tasks/ on index.md, core.md, python.md and java.md. Both pages were removed in 40d5fd3.
• Wrong outputs and samples that do not run:
  • get_classes() on Commons CLI prints 75, not 23.
  • The Python samples use a my_pkg project that does not exist.
  • The Java get_callers sample uses a short parameter type and returns {}.
  • The Python call-graph edge attribute is provenance, not prov.
• Missing facts:
  • the install commands and extras (cldk[java], cldk[neo4j]);
  • SYSTEM_PYTHON for a virtualenv;
  • which analysis level each method needs, and the silent empty results below that level;
  • how the cache behaves, and the TypeScript cache that ignores the level;
  • the exceptions a reader can see;
  • Neo4j prerequisites;
  • that Java analysis includes test sources.
• index.md says "Go and Rust are planned". The diagrams leave out CLDK.typescript().

Generated block (scripts/gen_api_docs.py):

• Signatures drop the keyword-only * marker on 57 methods. A positional call, as the page shows it, raises TypeError.
• Returns sections split one description into many bullets (103 of 124 sections).
• Reference text leaks into the output: Sphinx role fragments (class:~cldk...), :: markers, .. deprecated:: directives and --, which renders as an em-dash.
• Attribute descriptions are lost, and inherited fields and type aliases (TSType, TSClassAttribute and more) are missing.
• No entries exist for the types that signatures use: AnalysisLevel, the backend configs, the result models (LocateResult, Slice, EdgePage, FlowPaths, TaintResult and more), the exceptions in cldk.utils.exceptions, the Java projections and the tree-sitter helpers.
• The pages say "generated from cldk 2.0.0rc7". Regenerating from 2.0.0 supersedes docs(api): sync Python API reference to python-sdk 2.1.0 #8.

Related: #4.