docs: Update for comprehensive coverage and fix formatting

docs/api/behavioral.md

@@ -0,0 +1,24 @@
+# bead.behavioral
+
+Behavioral data analytics and extraction utilities for judgment experiment responses.
+
+## Analytics
+
+::: bead.behavioral.analytics
+    options:
+      show_root_heading: true
+      show_source: false
+
+## Extraction
+
+::: bead.behavioral.extraction
+    options:
+      show_root_heading: true
+      show_source: false
+
+## Merging
+
+::: bead.behavioral.merging
+    options:
+      show_root_heading: true
+      show_source: false

docs/api/data_collection.md

@@ -0,0 +1,24 @@
+# bead.data_collection
+
+Data retrieval and integration from JATOS and Prolific platforms.
+
+## JATOS Integration
+
+::: bead.data_collection.jatos
+    options:
+      show_root_heading: true
+      show_source: false
+
+## Prolific Integration
+
+::: bead.data_collection.prolific
+    options:
+      show_root_heading: true
+      show_source: false
+
+## Data Merging
+
+::: bead.data_collection.merger
+    options:
+      show_root_heading: true
+      show_source: false

docs/api/dsl.md

@@ -0,0 +1,45 @@
+# bead.dsl
+
+Domain-Specific Language for constraint expressions used in template slot filling and list partitioning.
+
+## Parser
+
+::: bead.dsl.parser
+    options:
+      show_root_heading: true
+      show_source: false
+
+## Evaluator
+
+::: bead.dsl.evaluator
+    options:
+      show_root_heading: true
+      show_source: false
+
+## Standard Library
+
+::: bead.dsl.stdlib
+    options:
+      show_root_heading: true
+      show_source: false
+
+## Abstract Syntax Tree
+
+::: bead.dsl.ast
+    options:
+      show_root_heading: true
+      show_source: false
+
+## Context
+
+::: bead.dsl.context
+    options:
+      show_root_heading: true
+      show_source: false
+
+## Errors
+
+::: bead.dsl.errors
+    options:
+      show_root_heading: true
+      show_source: false

docs/api/evaluation.md

@@ -0,0 +1,17 @@
+# bead.evaluation
+
+Metrics and evaluation utilities for convergence detection and inter-annotator agreement.
+
+## Convergence Detection
+
+::: bead.evaluation.convergence
+    options:
+      show_root_heading: true
+      show_source: false
+
+## Inter-Annotator Agreement
+
+::: bead.evaluation.interannotator
+    options:
+      show_root_heading: true
+      show_source: false

docs/api/items.md

@@ -100,3 +100,50 @@ Stage 3 of the bead pipeline: experimental item construction with 9 task types.
     options:
       show_root_heading: true
       show_source: false
+
+## Model Adapters
+
+::: bead.items.adapters.base
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.items.adapters.huggingface
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.items.adapters.openai
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.items.adapters.anthropic
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.items.adapters.google
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.items.adapters.togetherai
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.items.adapters.sentence_transformers
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.items.adapters.registry
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.items.adapters.api_utils
+    options:
+      show_root_heading: true
+      show_source: false

docs/api/participants.md

@@ -0,0 +1,31 @@
+# bead.participants
+
+Participant metadata models and collection management.
+
+## Models
+
+::: bead.participants.models
+    options:
+      show_root_heading: true
+      show_source: false
+
+## Collection
+
+::: bead.participants.collection
+    options:
+      show_root_heading: true
+      show_source: false
+
+## Merging
+
+::: bead.participants.merging
+    options:
+      show_root_heading: true
+      show_source: false
+
+## Metadata Specification
+
+::: bead.participants.metadata_spec
+    options:
+      show_root_heading: true
+      show_source: false

docs/api/resources.md

@@ -56,3 +56,30 @@ Stage 1 of the bead pipeline: lexical items, templates, and constraints.
     options:
       show_root_heading: true
       show_source: false
+
+## Resource Adapters
+
+::: bead.resources.adapters.base
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.resources.adapters.glazing
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.resources.adapters.unimorph
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.resources.adapters.cache
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.resources.adapters.registry
+    options:
+      show_root_heading: true
+      show_source: false

docs/api/simulation.md

@@ -0,0 +1,106 @@
+# bead.simulation
+
+Framework for simulating annotator responses with configurable noise models and task-specific strategies.
+
+## Runner
+
+::: bead.simulation.runner
+    options:
+      show_root_heading: true
+      show_source: false
+
+## Annotators
+
+::: bead.simulation.annotators.base
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.simulation.annotators.oracle
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.simulation.annotators.random
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.simulation.annotators.lm_based
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.simulation.annotators.distance_based
+    options:
+      show_root_heading: true
+      show_source: false
+
+## Noise Models
+
+::: bead.simulation.noise_models.base
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.simulation.noise_models.temperature
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.simulation.noise_models.random_noise
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.simulation.noise_models.systematic
+    options:
+      show_root_heading: true
+      show_source: false
+
+## Task-Specific Strategies
+
+::: bead.simulation.strategies.base
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.simulation.strategies.forced_choice
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.simulation.strategies.ordinal_scale
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.simulation.strategies.binary
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.simulation.strategies.categorical
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.simulation.strategies.multi_select
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.simulation.strategies.magnitude
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.simulation.strategies.free_text
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.simulation.strategies.cloze
+    options:
+      show_root_heading: true
+      show_source: false

docs/api/templates.md

@@ -32,3 +32,20 @@ Stage 2 of the bead pipeline: template filling strategies and constraint resolut
     options:
       show_root_heading: true
       show_source: false
+
+## Template Adapters
+
+::: bead.templates.adapters.base
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.templates.adapters.huggingface
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: bead.templates.adapters.cache
+    options:
+      show_root_heading: true
+      show_source: false