Description

Comprehensive documentation update to fix rendering issues and reflect the current state of the bead codebase.

Formatting fixes:

• Fix list rendering in architecture.md -- bold module headers were missing blank line separators, causing lists to render as inline text instead of bullet lists (14 sections fixed)
• Fix 12 instances of duplicated uv run uv run commands in testing.md

New API reference pages (6):

• bead.simulation -- annotators, noise models, task-specific strategies
• bead.evaluation -- convergence detection, inter-annotator agreement
• bead.dsl -- constraint expression parser, evaluator, stdlib, AST
• bead.behavioral -- judgment analytics, extraction, merging
• bead.participants -- participant metadata models and collections
• bead.data_collection -- JATOS and Prolific data retrieval

Expanded existing API pages with adapter coverage:

• items.md -- 9 model adapter entries (OpenAI, Anthropic, Google, HuggingFace, TogetherAI, etc.)
• resources.md -- 5 resource adapter entries (Glazing, UniMorph, etc.)
• templates.md -- 3 template adapter entries (HuggingFace MLM, etc.)

Content corrections:

• Updated module counts in architecture.md (14 -> 17 modules)
• Removed phantom files (model_metrics.py, cross_validation.py) from evaluation section that don't exist in codebase
• Added 3 missing modules to architecture: behavioral/, participants/, tokenization/
• Updated all task type references from 8 to 9 (added span labeling) across architecture.md, index.md, concepts.md
• Added 6 new entries to mkdocs.yml navigation

Motivation

Documentation was stale relative to the codebase -- several modules added since initial docs generation had no API reference pages, module counts were wrong, and list formatting was broken in the architecture page.

Type of Change

• Bug fix (non-breaking change that fixes an issue)
• New feature (non-breaking change that adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Documentation update
• Refactoring (no functional changes)
• Tests (adding or updating tests)

Checklist

• I have read the CONTRIBUTING guidelines
• My code follows the project's style guidelines
• I have run uv run ruff check . and uv run ruff format .
• I have run uv run pyright with no errors
• I have added tests that prove my fix/feature works
• All tests pass (uv run pytest tests/)
• I have updated documentation as needed

Testing

• mkdocs build completes with no errors (only pre-existing griffe warnings from Pydantic model docstrings)
• All 6 new API pages render correctly in the built site
• Verified list formatting fix resolves the inline-text rendering issue

Screenshots (if applicable)

N/A