agent-method 1.5.12

package/docs/internal/doc-tokens.yaml

@@ -0,0 +1,1103 @@
+# Documentation Token Registry
+# Single source of truth for values AND names that appear across documentation.
+# When a value or name changes, update this file FIRST, then propagate to all docs.
+#
+# NOTE: "tokens" in this file means tracked key-value pairs (feature counts, version
+# numbers, CLI commands, etc.) — NOT LLM tokens (the compute units consumed during
+# agent conversations). LLM token usage is tracked separately in SESSION-LOG.md.
+#
+# Four sections:
+#   tokens:              — values that change (CLI commands, version numbers, counts, thresholds)
+#   names:               — terminology that must stay consistent (concepts, workflows, stages, file roles)
+#   propagation_targets: — files known to use tokens/names from this registry
+#   doc_graph:           — document dependency graph (nodes + edges)
+#
+# Usage: Agent reads this file before writing or updating any docs/ file.
+# Cascade rule: when this file changes, check all docs/ for stale token values or name inconsistencies.
+# Last updated: 2026-03-15
+
+# ============================================================
+# SECTION 1: VALUES (things that change)
+# ============================================================
+tokens:
+  cli_command: "wwa"
+  npm_package: "agent-method"
+  pip_package: "wwa-tools"
+  npx_zero_install: "npx agent-method"
+  npm_global_install: "npm install -g agent-method"
+  pip_install: "pip install wwa-tools"
+  mcp_server_start: "npx agent-method serve"
+  watcher_start: "npx agent-method watch"
+  project_name: "wwa"
+  repo_url: "https://github.com/anthropics/wwa.git"
+  npm_version: "1.5.1"
+  registry_version: "v1.6"
+  feature_count: 36
+  domain_count: 8
+  directive_count: 10
+  workflow_count: 8
+  query_pattern_count: 29
+  lite_models: "Haiku, GPT-3.5, Gemini Flash"
+  standard_models: "Sonnet, GPT-4, Gemini Pro, Codex"
+  full_models: "Opus, o1, Gemini Ultra"
+  max_file_lines: 300
+  base_md_max_lines: 100
+  specialist_max_lines: 150
+  entry_point_target_lines: 60
+  starter_file_count: 20
+  full_file_count: 34
+  cmd_init: "wwa init"
+  cmd_check: "wwa check"
+  cmd_scan: "wwa scan"
+  cmd_route: "wwa route"
+  cmd_plan: "wwa plan"
+  cmd_implement: "wwa implement"
+  cmd_review: "wwa review"
+  cmd_digest: "wwa digest"
+  cmd_close: "wwa close"
+  cmd_refine: "wwa refine"
+  cmd_status: "wwa status"
+  cmd_upgrade: "wwa upgrade"
+  cmd_casestudy: "wwa casestudy"
+  cmd_docs: "wwa docs"
+  cmd_doc_review: "wwa doc-review"
+  cmd_deps: "wwa deps"
+  cmd_serve: "wwa serve"
+  cmd_watch: "wwa watch"
+  cmd_completion: "wwa completion"
+  cmd_project_discovery: "wwa project-discovery"
+  cmd_context_refresh: "wwa context-refresh"
+  cmd_phase_complete: "wwa phase-complete"
+  cmd_backlog: "wwa backlog"
+  cmd_plan_create: "wwa plan-create"
+  cmd_dependency_analysis: "wwa dependency-analysis"
+  cmd_debt_assessment: "wwa debt-assessment"
+  cmd_docs_update: "wwa docs-update"
+  cmd_cross_reference: "wwa cross-reference"
+  cmd_add: "wwa add"
+  developer_cmd_count: 26
+  pipeline_cmd_count: 5
+  server_cmd_count: 2
+  completion_cmd_count: 1
+  total_cmd_count: 34
+  node_min_version: "18"
+  python_min_version: "3.9"
+  last_close: "2026-03-16"
+  methodology_file_count: 383
+  docs_file_count: 80
+  context_file_count: 6
+  session_count: 1
+  decision_count: 202
+  total_features_referenced: 0
+  files_near_threshold: 1
+  files_over_threshold: 1
+
+# ============================================================
+# SECTION 2: NAMES (terminology that must stay consistent)
+# ============================================================
+names:
+  workflow_stages:
+    - canonical: Initialize
+      aliases:
+        - init
+        - cold start
+        - session start
+      context: First stage. Agent loads entry point + STATE.md.
+    - canonical: Scope
+      aliases:
+        - scoping
+        - query classification
+      context: Agent classifies query against scoping table, loads relevant files.
+    - canonical: Plan
+      aliases:
+        - planning
+        - task planning
+      context: Agent proposes structured plan. Primary checkpoint.
+    - canonical: Execute
+      aliases:
+        - execution
+        - implement
+        - implementation
+      context: Agent implements approved plan. Records decisions in STATE.md.
+    - canonical: Verify
+      aliases:
+        - verification
+        - validation
+      context: Agent checks work against plan criteria.
+    - canonical: Close
+      aliases:
+        - session close
+        - wrap-up
+      context: Agent writes SUMMARY.md entry, updates STATE.md position.
+  interaction_levels:
+    - canonical: autonomous
+      context: Routine, low-risk work. Agent handles independently.
+    - canonical: checkpoint
+      context: Default. Approve plan, trust execution, report at completion.
+    - canonical: collaborative
+      context: Complex tasks. Iterate on each step.
+    - canonical: supervised
+      context: Learning methodology, high-risk, or debugging.
+  integration_profiles:
+    - canonical: lite
+      aliases:
+        - Lite
+      context: Minimal rules, STATE.md only, 2 cascade rules. For Haiku, GPT-3.5, Gemini Flash.
+    - canonical: standard
+      aliases:
+        - Standard
+      context: Default. Core rules + context pairing, overflow to METHODOLOGY.md. For Sonnet, GPT-4, Gemini Pro, Codex.
+    - canonical: full
+      aliases:
+        - Full
+      context: All rules inline, all intelligence layer files. For Opus, o1, Gemini Ultra.
+  template_tiers:
+    - canonical: starter
+      aliases:
+        - Starter
+      context: 7 files. Entry point, PROJECT.md, STATE.md, ROADMAP.md, PLAN.md, .context/BASE.md, PROJECT-PROFILE.md.
+    - canonical: full
+      aliases:
+        - Full
+      context: 11+ files. Adds REQUIREMENTS.md, SUMMARY.md, .context/REGISTRY.md, .context/COMPOSITION.md, todos/backlog.md.
+  project_types:
+    - canonical: general
+      cli_alias: general
+      context: Universal rules only. No extensions.
+    - canonical: code
+      cli_alias: code
+      context: Software development. Code change, bug fix, dependency, database, API, deployment.
+    - canonical: data
+      cli_alias: data
+      context: Dataset analysis, document exploration. Data ingest, schema, exploration.
+    - canonical: analytical
+      cli_alias: context
+      context: Research, evaluation, prompt/context work. Chain work, evaluation, composition.
+    - canonical: mixed
+      cli_alias: mix
+      context: Multiple extensions combined. Code + data, code + analytical.
+  guided_workflows:
+    - id: WF-01
+      canonical: standard-task
+      display: Standard task
+      context: Review → Plan → Implement → Document → Update. Default for general queries.
+    - id: WF-02
+      canonical: code-change
+      display: Code change
+      context: Review → Plan → Implement → Context-sync → Update. Code projects.
+    - id: WF-03
+      canonical: context-refresh
+      display: Context refresh
+      context: Scan → Compare → Update context → Cascade → Record.
+    - id: WF-04
+      canonical: agent-guided-onboarding
+      display: Agent-guided onboarding
+      aliases:
+        - bootstrap
+        - first session
+      context: Ask → Populate → Confirm. Greenfield (4 stages) and brownfield (5 stages).
+    - id: WF-05
+      canonical: data-exploration
+      display: Data exploration
+      context: Ingest → Map → Reference → Explore → Refine. Data projects.
+    - id: WF-06
+      canonical: analytical-system
+      display: Analytical system
+      context: Discover → Map chains → Build context → Compose → Evaluate → Refine.
+    - id: WF-07
+      canonical: specification-project
+      display: Specification project
+      context: For spec writing projects.
+    - id: WF-08
+      canonical: discovery
+      display: Discovery
+      aliases:
+        - brownfield discovery
+      context: Inventory → Map → Extract → Assess → Bootstrap. Brownfield projects.
+  feature_domains:
+    - id: CTX
+      canonical: Context management
+      feature_range: CTX-01 through CTX-06
+      context: Bootstrap, maintain, evolve .context/ files.
+    - id: QRY
+      canonical: Query routing
+      feature_range: QRY-01 through QRY-03
+      context: Session init, query classification, cascade propagation.
+    - id: STT
+      canonical: State management
+      feature_range: STT-01 through STT-03
+      context: Decision capture, uncertainty tracking, position tracking.
+    - id: TSK
+      canonical: Task execution
+      feature_range: TSK-01 through TSK-04
+      context: Planning, verification, session close, audit trail.
+    - id: HAI
+      canonical: Human-agent interaction
+      feature_range: HAI-01 through HAI-06
+      context: Checkpoints, interaction levels, audience separation, docs triggers, model capability, write obligations.
+    - id: TPL
+      canonical: Template and bootstrap
+      feature_range: TPL-01 through TPL-03
+      context: Project init, runtime detection, structure selection.
+    - id: EXP
+      canonical: Data exploration
+      feature_range: EXP-01 through EXP-04
+      context: Data ingest, reference building, exploration commands, abstraction management.
+    - id: SCAN
+      canonical: Project discovery
+      aliases:
+        - Brownfield discovery
+      feature_range: SCAN-01 through SCAN-07
+      context: >-
+        Codebase inventory, dependency mapping, pattern extraction, debt assessment, document dependency graph, document
+        registry generation, configurable boundaries.
+  protocol_directives:
+    - id: P-01
+      canonical: Build understanding
+      short: Every change is also a context change
+    - id: P-02
+      canonical: Maintain for future self
+      short: Record decisions in STATE.md in the SAME response
+    - id: P-03
+      canonical: Cascade is not optional
+      short: After every file change, check the cascade table
+    - id: P-04
+      canonical: Scope to avoid drowning
+      short: Load BASE.md + one specialist per query
+    - id: P-05
+      canonical: Surface uncertainty
+      short: Surface uncertainty as open questions in STATE.md
+    - id: P-06
+      canonical: Human controls direction
+      short: Propose plans and wait for approval
+    - id: P-07
+      canonical: Keep files loadable
+      short: Intelligence layer files under 300 lines
+    - id: P-08
+      canonical: Methodology is additive only
+      short: Never modify source code, never delete existing files
+    - id: P-09
+      canonical: Surface capability limitations
+      short: Agent self-monitors and alerts user to degradation
+    - id: P-10
+      canonical: Document proportionally
+      short: Match documentation effort to task significance
+  methodology_concepts:
+    - canonical: context pairing
+      aliases:
+        - BASE + specialist model
+      context: Loading BASE.md + one specialist file per query type.
+    - canonical: dependency cascade
+      aliases:
+        - cascade
+        - cascade table
+        - cascade rules
+      context: When X changes, also update Y. Prevents file drift.
+    - canonical: scoping rules
+      aliases:
+        - scoping table
+        - query routing
+      context: Query type → file set mapping in entry point.
+    - canonical: intelligence layer
+      aliases:
+        - project intelligence layer
+      context: PROJECT/STATE/REQUIREMENTS/ROADMAP/PLAN/SUMMARY files.
+    - canonical: interaction level
+      context: "Configurable checkpoint density: autonomous/checkpoint/collaborative/supervised."
+    - canonical: entry point
+      aliases:
+        - agent entry point
+      context: Auto-loaded file (CLAUDE.md/.cursorrules/AGENT.md) with scoping + cascade.
+    - canonical: specialist context
+      aliases:
+        - specialist file
+        - specialist
+      context: Domain-specific .context/ file loaded per scoping rule.
+    - canonical: phase gate
+      aliases:
+        - gate
+        - gate criteria
+      context: Testable criteria that define done per phase.
+    - canonical: codebase map
+      context: Table of paths, purposes, patterns in BASE.md for code projects.
+    - canonical: context refresh
+      context: Agent rescans project and updates .context/ files.
+    - canonical: scale management
+      aliases:
+        - file splitting
+        - index + components
+      context: When files exceed 300 lines, split into index + components subdirectory.
+  intelligence_layer_files:
+    - file: PROJECT.md
+      role: Project vision, audiences, principles
+      audience: human
+    - file: PROJECT-PROFILE.md
+      role: Project type, lifecycle stage, active extensions
+      audience: agent
+    - file: STATE.md
+      role: Current position, decisions, blockers, open questions
+      audience: both
+    - file: REQUIREMENTS.md
+      role: Formal requirements with traceability
+      tier: full
+    - file: ROADMAP.md
+      role: Phase breakdown with deliverables and gate criteria
+      audience: both
+    - file: PLAN.md
+      role: Current atomic task with verification criteria
+      audience: agent
+    - file: SUMMARY.md
+      role: Session audit trail (chronological record of work done)
+      audience: both
+    - file: SESSION-LOG.md
+      role: Session metrics and refinement tracking
+      audience: agent
+    - file: .context/BASE.md
+      role: System model, always loaded with entry point
+      audience: agent
+    - file: .context/REGISTRY.md
+      role: Navigation registry for split file trees
+      tier: full
+    - file: .context/PROTOCOL.yaml
+      role: Agent protocol — scoping, cascade, conventions, close-check obligations
+      audience: agent
+    - file: .context/INDEX.yaml
+      role: Navigation manifest — file inventory, project metadata, live metrics
+      audience: agent
+    - file: .context/METHODOLOGY.md
+      role: Onboarding protocol and format specs (loaded on-demand)
+      audience: agent
+    - file: Management/DIGEST.md
+      role: High-effort task digest for managers and leads
+      audience: human
+    - file: Management/STATUS.md
+      role: Project health snapshot — phase, blockers, decisions, risk
+      audience: human
+    - file: Reviews/INDEX.md
+      role: Synthesized project intelligence dashboard
+      audience: both
+    - file: agentWorkflows/INDEX.md
+      role: Agent workflow performance overview
+      audience: both
+  communication_points:
+    - canonical: direction
+      context: Human → agent. Drives work. Queries, approvals, redirects.
+    - canonical: checkpoint
+      context: Agent → human. Surfaces state. Plans, status, questions.
+    - canonical: record
+      context: Persistent artifacts. STATE.md, SUMMARY.md, .context/ files.
+  interaction_patterns:
+    - canonical: Cold start
+      aliases:
+        - session start
+        - initialization
+      context: "Two-file load: entry point + STATE.md."
+    - canonical: Scoped reading
+      aliases:
+        - query scoping
+      context: Query classification → file set loading.
+    - canonical: Decision recording
+      context: Immediate capture in STATE.md decisions table.
+    - canonical: Cascade updating
+      context: Post-change propagation via cascade table.
+    - canonical: Uncertainty flagging
+      context: Open questions surfaced in STATE.md.
+    - canonical: Audit trail
+      context: SUMMARY.md session entries at close.
+    - canonical: Session metrics
+      context: Effort, ambiguity, context, tokens, time, user response tracking.
+  entry_point_runtimes:
+    - file: CLAUDE.md
+      runtime: Claude Code
+      auto_loaded: true
+    - file: .cursorrules
+      runtime: Cursor
+      aliases:
+        - Cursor Composer
+      auto_loaded: true
+    - file: AGENT.md
+      runtime: Other
+      aliases:
+        - Gemini
+        - Codex
+        - Cline
+        - Aider
+      auto_loaded: false
+      note: Paste or reference manually
+
+# ============================================================
+# SECTION 3: PROPAGATION TRACKING
+# ============================================================
+propagation_targets:
+  docs:
+    - docs/guides/quick-start.md
+    - docs/guides/for-developers.md
+    - docs/guides/for-developers/cli-tools.md
+    - docs/guides/for-managers.md
+    - docs/guides/mcp-integration.md
+    - docs/index.md
+    - docs/architecture/file-roles.md
+    - docs/architecture/scoping-rules.md
+    - docs/architecture/dependency-cascade.md
+    - docs/architecture/context-pairing.md
+    - docs/architecture/integration-profiles.md
+    - docs/architecture/project-lifecycle.md
+    - docs/architecture/feature-tree.md
+    - docs/architecture/workflow-extensions.md
+    - docs/workflow/stages.md
+    - docs/workflow/interaction-patterns.md
+    - docs/workflow/communication-points.md
+    - docs/workflow/human-agent-contract.md
+    - docs/workflow/session-protocol.md
+    - docs/workflow/task-structure.md
+  templates:
+    - templates/README.md
+    - templates/starter/CLAUDE.md
+    - templates/starter/AGENT.md
+    - templates/starter/.cursorrules
+    - templates/full/CLAUDE.md
+    - templates/full/AGENT.md
+    - templates/full/.cursorrules
+    - templates/entry-points/CLAUDE.md
+    - templates/entry-points/AGENT.md
+    - templates/entry-points/.cursorrules
+    - templates/extensions/code-project.md
+    - templates/extensions/data-exploration.md
+    - templates/extensions/analytical-system.md
+    - templates/extensions/MANIFEST.md
+    - templates/starter/.context/PROTOCOL.yaml
+    - templates/full/.context/PROTOCOL.yaml
+    - templates/starter/.context/INDEX.yaml
+    - templates/full/.context/INDEX.yaml
+  project:
+    - README.md
+    - PROJECT.md
+    - CHANGELOG.md
+    - REQUIREMENTS.md
+  case_studies:
+    - case-studies/framework.md
+  internal:
+    - docs/internal/features.md
+    - docs/internal/feature-registry.yaml
+    - docs/internal/doc-update-policy.md
+    - docs/internal/docs-navigation-agent.md
+
+# ============================================================
+# SECTION 4: DOCUMENT DEPENDENCY GRAPH
+# ============================================================
+# Nodes: array of {path, category, role} for every docs/ file.
+# Edges: array of {from, to, type} — typed relationships.
+# Used by: wwa deps, wwa doc-review, wwa close (orphan detection).
+doc_graph:
+  last_scan: "2026-03-16"
+  nodes:
+    - path: docs/index.md
+      category: hub
+      role: Documentation hub — audience, topic, and integration views
+    - path: docs/architecture/context-pairing.md
+      category: architecture
+      role: Context pairing specification — BASE + specialist model
+    - path: docs/architecture/context-pairing/examples-and-lifecycle.md
+      category: architecture
+      role: Context pairing examples and maintenance lifecycle
+    - path: docs/architecture/dependency-cascade.md
+      category: architecture
+      role: Dependency cascade specification — when X changes update Y
+    - path: docs/architecture/feature-tree.md
+      category: architecture
+      role: Feature tree index — domains, features, workflows, directives
+    - path: docs/architecture/feature-tree/activation-tables.md
+      category: architecture
+      role: Feature activation by lifecycle stage and project type
+    - path: docs/architecture/feature-tree/cross-reference.md
+      category: architecture
+      role: Feature cross-reference — features to files and config
+    - path: docs/architecture/feature-tree/dependencies-and-domains.md
+      category: architecture
+      role: Feature dependencies and domain groupings
+    - path: docs/architecture/feature-tree/workflows.md
+      category: architecture
+      role: Guided workflow definitions (WF-01 through WF-08)
+    - path: docs/architecture/file-roles.md
+      category: architecture
+      role: Intelligence layer file roles and format specifications
+    - path: docs/architecture/integration-profiles.md
+      category: architecture
+      role: Integration profiles — lite, standard, full tiers
+    - path: docs/architecture/project-lifecycle.md
+      category: architecture
+      role: Project lifecycle stages and transitions
+    - path: docs/architecture/scoping-rules.md
+      category: architecture
+      role: Scoping rules — query type to file set mapping
+    - path: docs/architecture/workflow-extensions.md
+      category: architecture
+      role: Project-type workflow extensions (code, data, analytical)
+    - path: docs/workflow/communication-points.md
+      category: workflow
+      role: Communication point types — direction, checkpoint, record
+    - path: docs/workflow/human-agent-contract.md
+      category: workflow
+      role: Human-agent contract — responsibilities and boundaries
+    - path: docs/workflow/interaction-patterns.md
+      category: workflow
+      role: Interaction patterns — cold start, scoped reading, cascade
+    - path: docs/workflow/session-protocol.md
+      category: workflow
+      role: Session protocol — init through close sequence
+    - path: docs/workflow/stages.md
+      category: workflow
+      role: Workflow stages — Initialize, Scope, Plan, Execute, Verify, Close
+    - path: docs/workflow/task-structure.md
+      category: workflow
+      role: Task structure — atomic tasks with verification criteria
+    - path: docs/guides/for-developers.md
+      category: guides
+      role: Developer guide index — setup, configuration, CLI tools
+    - path: docs/guides/for-developers/cli-tools.md
+      category: guides
+      role: CLI tools deep dive — installation, usage, examples
+    - path: docs/guides/for-developers/command-reference.md
+      category: guides
+      role: CLI command reference — all commands with options
+    - path: docs/guides/for-managers.md
+      category: guides
+      role: Manager guide — reading project health from methodology files
+    - path: docs/guides/mcp-integration.md
+      category: guides
+      role: MCP server integration guide
+    - path: docs/guides/quick-start.md
+      category: guides
+      role: Quick start — copy template, fill PROJECT.md, start working
+    - path: docs/guides/rendered-examples/base-context-example.md
+      category: guides
+      role: Rendered example — populated BASE.md
+    - path: docs/guides/rendered-examples/plan-example.md
+      category: guides
+      role: Rendered example — populated PLAN.md
+    - path: docs/guides/rendered-examples/roadmap-example.md
+      category: guides
+      role: Rendered example — populated ROADMAP.md
+    - path: docs/guides/rendered-examples/state-example.md
+      category: guides
+      role: Rendered example — populated STATE.md
+    - path: docs/guides/rendered-examples/summary-example.md
+      category: guides
+      role: Rendered example — populated SUMMARY.md
+    - path: docs/internal/doc-registry.md
+      category: internal
+      role: Generated document registry — human-readable summary
+    - path: docs/internal/doc-registry.yaml
+      category: internal
+      role: Generated document registry — machine-readable YAML
+    - path: docs/internal/doc-tokens.yaml
+      category: internal
+      role: Token registry — single source of truth for values and names
+    - path: docs/internal/doc-update-policy.md
+      category: internal
+      role: Documentation update policy — materiality thresholds
+    - path: docs/internal/docs-navigation-agent.md
+      category: internal
+      role: Agent navigation guide — how to find docs by topic
+    - path: docs/internal/entry-point-derivation.md
+      category: internal
+      role: Entry point derivation specification from feature registry
+    - path: docs/internal/entry-point-derivation/worked-example-and-extensions.md
+      category: internal
+      role: Entry point derivation worked example and extension rules
+    - path: docs/internal/feature-domain-map.md
+      category: internal
+      role: Feature domain map — research grounding per domain
+    - path: docs/internal/feature-interactions.md
+      category: internal
+      role: Feature interaction index — how features compose
+    - path: docs/internal/feature-interactions/activation-and-dependencies.md
+      category: internal
+      role: Feature activation rules and dependency chains
+    - path: docs/internal/feature-interactions/bootstrap.md
+      category: internal
+      role: Feature interactions during project bootstrap
+    - path: docs/internal/feature-interactions/cascading.md
+      category: internal
+      role: Feature interactions during cascade propagation
+    - path: docs/internal/feature-interactions/context-refresh.md
+      category: internal
+      role: Feature interactions during context refresh
+    - path: docs/internal/feature-interactions/session-lifecycle.md
+      category: internal
+      role: Feature interactions across session lifecycle
+    - path: docs/internal/feature-registry.yaml
+      category: internal
+      role: Feature registry — canonical feature definitions, domains, workflows
+    - path: docs/internal/features.md
+      category: internal
+      role: Feature catalog index — all features with domain grouping
+    - path: docs/internal/features/cross-domain.md
+      category: internal
+      role: Cross-domain features — SCAN, protocol directives
+    - path: docs/internal/features/ctx-context-management.md
+      category: internal
+      role: CTX domain features — context bootstrap and maintenance
+    - path: docs/internal/features/exp-data-exploration.md
+      category: internal
+      role: EXP domain features — data exploration capabilities
+    - path: docs/internal/features/hai-human-agent-interaction.md
+      category: internal
+      role: HAI domain features — checkpoints, levels, audiences
+    - path: docs/internal/features/qry-query-routing.md
+      category: internal
+      role: QRY domain features — query classification and routing
+    - path: docs/internal/features/stt-state-management.md
+      category: internal
+      role: STT domain features — decision and state tracking
+    - path: docs/internal/features/tpl-template-bootstrap.md
+      category: internal
+      role: TPL domain features — template init and detection
+    - path: docs/internal/features/tsk-task-execution.md
+      category: internal
+      role: TSK domain features — planning, verification, close
+    - path: docs/internal/gate-protocol.md
+      category: internal
+      role: Gate protocol — phase gate testing and transition rules
+    - path: docs/internal/pipeline-stages.md
+      category: internal
+      role: Pipeline stages index — bootstrap, runtime, tooling
+    - path: docs/internal/pipeline-stages/bootstrap-pipeline.md
+      category: internal
+      role: Bootstrap pipeline — project init sequence
+    - path: docs/internal/pipeline-stages/runtime-pipeline.md
+      category: internal
+      role: Runtime pipeline — per-query execution
+    - path: docs/internal/pipeline-stages/tooling-pipeline.md
+      category: internal
+      role: Tooling pipeline — CLI tool execution
+    - path: docs/internal/protocol-tools.md
+      category: internal
+      role: Protocol tools index — compliance, drift, workflow, telemetry, capability
+    - path: docs/internal/protocol-tools/cross-tool-integration.md
+      category: internal
+      role: Cross-tool integration patterns
+    - path: docs/internal/protocol-tools/tool-1-compliance.md
+      category: internal
+      role: Tool 1 — compliance checker specification
+    - path: docs/internal/protocol-tools/tool-2-drift.md
+      category: internal
+      role: Tool 2 — drift detector specification
+    - path: docs/internal/protocol-tools/tool-3-workflow.md
+      category: internal
+      role: Tool 3 — workflow tracker specification
+    - path: docs/internal/protocol-tools/tool-4-telemetry.md
+      category: internal
+      role: Tool 4 — telemetry collector specification
+    - path: docs/internal/protocol-tools/tool-5-capability.md
+      category: internal
+      role: Tool 5 — capability profiler specification
+    - path: docs/internal/quick-start-walkthrough.md
+      category: internal
+      role: Internal quick start walkthrough — dev-facing setup guide
+    - path: docs/internal/rendered-examples-methodology.md
+      category: internal
+      role: Rendered examples methodology — how examples are constructed
+    - path: docs/internal/routing-algorithm.md
+      category: internal
+      role: Routing algorithm index — classify, resolve, cascade
+    - path: docs/internal/routing-algorithm/cascade-execution.md
+      category: internal
+      role: Routing algorithm — cascade execution phase
+    - path: docs/internal/routing-algorithm/classification.md
+      category: internal
+      role: Routing algorithm — query classification phase
+    - path: docs/internal/routing-algorithm/edge-cases-integration.md
+      category: internal
+      role: Routing algorithm — edge cases and integration
+    - path: docs/internal/routing-algorithm/resolution.md
+      category: internal
+      role: Routing algorithm — file resolution phase
+    - path: ".context/BASE.md"
+      category: "context"
+      role: "detected at close — review during next session"
+    - path: ".context/PROTOCOL.yaml"
+      category: "context"
+      role: "detected at close — review during next session"
+    - path: ".context/METHODOLOGY.md"
+      category: "context"
+      role: "detected at close — review during next session"
+    - path: ".context/INDEX.yaml"
+      category: "context"
+      role: "detected at close — review during next session"
+  edges:
+    - from: docs/index.md
+      to: docs/internal/docs-navigation-agent.md
+      type: references
+    - from: docs/architecture/feature-tree.md
+      to: docs/architecture/feature-tree/dependencies-and-domains.md
+      type: references
+    - from: docs/architecture/feature-tree.md
+      to: docs/architecture/feature-tree/workflows.md
+      type: references
+    - from: docs/architecture/feature-tree.md
+      to: docs/architecture/feature-tree/cross-reference.md
+      type: references
+    - from: docs/architecture/feature-tree.md
+      to: docs/architecture/feature-tree/activation-tables.md
+      type: references
+    - from: docs/architecture/project-lifecycle.md
+      to: docs/architecture/file-roles.md
+      type: depends_on
+    - from: docs/architecture/project-lifecycle.md
+      to: docs/architecture/integration-profiles.md
+      type: depends_on
+    - from: docs/architecture/integration-profiles.md
+      to: docs/architecture/project-lifecycle.md
+      type: references
+    - from: docs/architecture/scoping-rules.md
+      to: docs/architecture/context-pairing.md
+      type: references
+    - from: docs/architecture/scoping-rules.md
+      to: docs/architecture/project-lifecycle.md
+      type: references
+    - from: docs/architecture/scoping-rules.md
+      to: docs/internal/routing-algorithm.md
+      type: references
+    - from: docs/architecture/dependency-cascade.md
+      to: docs/internal/routing-algorithm.md
+      type: references
+    - from: docs/architecture/context-pairing.md
+      to: docs/architecture/context-pairing/examples-and-lifecycle.md
+      type: references
+    - from: docs/architecture/context-pairing/examples-and-lifecycle.md
+      to: docs/architecture/scoping-rules.md
+      type: references
+    - from: docs/architecture/context-pairing/examples-and-lifecycle.md
+      to: docs/architecture/context-pairing.md
+      type: depends_on
+    - from: docs/architecture/file-roles.md
+      to: docs/architecture/context-pairing.md
+      type: extends
+    - from: docs/architecture/feature-tree/dependencies-and-domains.md
+      to: docs/architecture/feature-tree.md
+      type: references
+    - from: docs/architecture/feature-tree/workflows.md
+      to: docs/architecture/feature-tree.md
+      type: references
+    - from: docs/architecture/feature-tree/cross-reference.md
+      to: docs/architecture/feature-tree.md
+      type: references
+    - from: docs/architecture/feature-tree/activation-tables.md
+      to: docs/architecture/project-lifecycle.md
+      type: references
+    - from: docs/architecture/feature-tree/activation-tables.md
+      to: docs/architecture/feature-tree.md
+      type: references
+    - from: docs/workflow/stages.md
+      to: docs/workflow/session-protocol.md
+      type: references
+    - from: docs/workflow/stages.md
+      to: docs/workflow/communication-points.md
+      type: references
+    - from: docs/workflow/stages.md
+      to: docs/workflow/human-agent-contract.md
+      type: references
+    - from: docs/workflow/stages.md
+      to: docs/workflow/interaction-patterns.md
+      type: references
+    - from: docs/workflow/stages.md
+      to: docs/workflow/task-structure.md
+      type: references
+    - from: docs/workflow/communication-points.md
+      to: docs/workflow/stages.md
+      type: references
+    - from: docs/workflow/communication-points.md
+      to: docs/workflow/human-agent-contract.md
+      type: references
+    - from: docs/workflow/communication-points.md
+      to: docs/workflow/interaction-patterns.md
+      type: references
+    - from: docs/workflow/communication-points.md
+      to: docs/workflow/session-protocol.md
+      type: references
+    - from: docs/workflow/human-agent-contract.md
+      to: docs/workflow/stages.md
+      type: references
+    - from: docs/workflow/human-agent-contract.md
+      to: docs/workflow/communication-points.md
+      type: references
+    - from: docs/workflow/human-agent-contract.md
+      to: docs/workflow/session-protocol.md
+      type: references
+    - from: docs/workflow/human-agent-contract.md
+      to: docs/workflow/interaction-patterns.md
+      type: references
+    - from: docs/workflow/interaction-patterns.md
+      to: docs/workflow/stages.md
+      type: references
+    - from: docs/workflow/interaction-patterns.md
+      to: docs/workflow/communication-points.md
+      type: references
+    - from: docs/workflow/interaction-patterns.md
+      to: docs/workflow/human-agent-contract.md
+      type: references
+    - from: docs/workflow/interaction-patterns.md
+      to: docs/workflow/session-protocol.md
+      type: references
+    - from: docs/workflow/session-protocol.md
+      to: docs/workflow/stages.md
+      type: references
+    - from: docs/workflow/session-protocol.md
+      to: docs/workflow/communication-points.md
+      type: references
+    - from: docs/workflow/session-protocol.md
+      to: docs/workflow/human-agent-contract.md
+      type: references
+    - from: docs/workflow/session-protocol.md
+      to: docs/workflow/interaction-patterns.md
+      type: references
+    - from: docs/workflow/session-protocol.md
+      to: docs/workflow/task-structure.md
+      type: references
+    - from: docs/workflow/task-structure.md
+      to: docs/workflow/stages.md
+      type: references
+    - from: docs/workflow/task-structure.md
+      to: docs/workflow/session-protocol.md
+      type: references
+    - from: docs/workflow/task-structure.md
+      to: docs/workflow/human-agent-contract.md
+      type: references
+    - from: docs/guides/quick-start.md
+      to: docs/guides/for-developers.md
+      type: references
+    - from: docs/guides/quick-start.md
+      to: docs/guides/rendered-examples/state-example.md
+      type: references
+    - from: docs/guides/for-developers.md
+      to: docs/guides/quick-start.md
+      type: references
+    - from: docs/guides/for-developers.md
+      to: docs/guides/for-developers/cli-tools.md
+      type: references
+    - from: docs/guides/for-developers.md
+      to: docs/guides/for-developers/command-reference.md
+      type: references
+    - from: docs/guides/for-developers.md
+      to: docs/guides/mcp-integration.md
+      type: references
+    - from: docs/guides/for-developers.md
+      to: docs/architecture/file-roles.md
+      type: references
+    - from: docs/guides/for-developers.md
+      to: docs/architecture/scoping-rules.md
+      type: references
+    - from: docs/guides/for-developers.md
+      to: docs/architecture/context-pairing.md
+      type: references
+    - from: docs/guides/for-developers.md
+      to: docs/workflow/session-protocol.md
+      type: references
+    - from: docs/guides/for-developers.md
+      to: docs/workflow/task-structure.md
+      type: references
+    - from: docs/guides/for-developers/cli-tools.md
+      to: docs/guides/mcp-integration.md
+      type: references
+    - from: docs/guides/for-developers/command-reference.md
+      to: docs/guides/for-developers/cli-tools.md
+      type: references
+    - from: docs/guides/for-managers.md
+      to: docs/guides/rendered-examples/state-example.md
+      type: references
+    - from: docs/guides/for-managers.md
+      to: docs/guides/rendered-examples/roadmap-example.md
+      type: references
+    - from: docs/guides/for-managers.md
+      to: docs/guides/rendered-examples/summary-example.md
+      type: references
+    - from: docs/internal/docs-navigation-agent.md
+      to: docs/internal/features.md
+      type: references
+    - from: docs/internal/docs-navigation-agent.md
+      to: docs/internal/feature-registry.yaml
+      type: references
+    - from: docs/internal/docs-navigation-agent.md
+      to: docs/internal/routing-algorithm.md
+      type: references
+    - from: docs/internal/docs-navigation-agent.md
+      to: docs/internal/entry-point-derivation.md
+      type: references
+    - from: docs/internal/docs-navigation-agent.md
+      to: docs/internal/pipeline-stages.md
+      type: references
+    - from: docs/internal/docs-navigation-agent.md
+      to: docs/internal/rendered-examples-methodology.md
+      type: references
+    - from: docs/internal/docs-navigation-agent.md
+      to: docs/internal/quick-start-walkthrough.md
+      type: references
+    - from: docs/internal/features.md
+      to: docs/internal/feature-interactions.md
+      type: references
+    - from: docs/internal/features.md
+      to: docs/internal/features/ctx-context-management.md
+      type: depends_on
+    - from: docs/internal/features.md
+      to: docs/internal/features/qry-query-routing.md
+      type: depends_on
+    - from: docs/internal/features.md
+      to: docs/internal/features/stt-state-management.md
+      type: depends_on
+    - from: docs/internal/features.md
+      to: docs/internal/features/tsk-task-execution.md
+      type: depends_on
+    - from: docs/internal/features.md
+      to: docs/internal/features/hai-human-agent-interaction.md
+      type: depends_on
+    - from: docs/internal/features.md
+      to: docs/internal/features/tpl-template-bootstrap.md
+      type: depends_on
+    - from: docs/internal/features.md
+      to: docs/internal/features/exp-data-exploration.md
+      type: depends_on
+    - from: docs/internal/features.md
+      to: docs/internal/features/cross-domain.md
+      type: depends_on
+    - from: docs/internal/feature-interactions.md
+      to: docs/internal/feature-interactions/session-lifecycle.md
+      type: depends_on
+    - from: docs/internal/feature-interactions.md
+      to: docs/internal/feature-interactions/bootstrap.md
+      type: depends_on
+    - from: docs/internal/feature-interactions.md
+      to: docs/internal/feature-interactions/context-refresh.md
+      type: depends_on
+    - from: docs/internal/feature-interactions.md
+      to: docs/internal/feature-interactions/cascading.md
+      type: depends_on
+    - from: docs/internal/feature-interactions.md
+      to: docs/internal/feature-interactions/activation-and-dependencies.md
+      type: depends_on
+    - from: docs/internal/entry-point-derivation.md
+      to: docs/internal/feature-registry.yaml
+      type: depends_on
+    - from: docs/internal/entry-point-derivation.md
+      to: docs/internal/routing-algorithm.md
+      type: depends_on
+    - from: docs/internal/entry-point-derivation.md
+      to: docs/internal/entry-point-derivation/worked-example-and-extensions.md
+      type: depends_on
+    - from: docs/internal/entry-point-derivation/worked-example-and-extensions.md
+      to: docs/internal/feature-registry.yaml
+      type: references
+    - from: docs/internal/entry-point-derivation/worked-example-and-extensions.md
+      to: docs/internal/routing-algorithm.md
+      type: references
+    - from: docs/internal/routing-algorithm.md
+      to: docs/internal/feature-registry.yaml
+      type: depends_on
+    - from: docs/internal/routing-algorithm.md
+      to: docs/internal/feature-domain-map.md
+      type: references
+    - from: docs/internal/routing-algorithm.md
+      to: docs/internal/routing-algorithm/classification.md
+      type: depends_on
+    - from: docs/internal/routing-algorithm.md
+      to: docs/internal/routing-algorithm/resolution.md
+      type: depends_on
+    - from: docs/internal/routing-algorithm.md
+      to: docs/internal/routing-algorithm/cascade-execution.md
+      type: depends_on
+    - from: docs/internal/routing-algorithm.md
+      to: docs/internal/routing-algorithm/edge-cases-integration.md
+      type: depends_on
+    - from: docs/internal/routing-algorithm/classification.md
+      to: docs/internal/routing-algorithm.md
+      type: references
+    - from: docs/internal/routing-algorithm/resolution.md
+      to: docs/internal/routing-algorithm.md
+      type: references
+    - from: docs/internal/routing-algorithm/cascade-execution.md
+      to: docs/internal/routing-algorithm.md
+      type: references
+    - from: docs/internal/routing-algorithm/edge-cases-integration.md
+      to: docs/internal/routing-algorithm.md
+      type: references
+    - from: docs/internal/pipeline-stages.md
+      to: docs/internal/feature-registry.yaml
+      type: depends_on
+    - from: docs/internal/pipeline-stages.md
+      to: docs/internal/routing-algorithm.md
+      type: references
+    - from: docs/internal/pipeline-stages.md
+      to: docs/internal/entry-point-derivation.md
+      type: references
+    - from: docs/internal/pipeline-stages.md
+      to: docs/internal/pipeline-stages/runtime-pipeline.md
+      type: depends_on
+    - from: docs/internal/pipeline-stages.md
+      to: docs/internal/pipeline-stages/tooling-pipeline.md
+      type: depends_on
+    - from: docs/internal/pipeline-stages.md
+      to: docs/internal/pipeline-stages/bootstrap-pipeline.md
+      type: depends_on
+    - from: docs/internal/pipeline-stages/runtime-pipeline.md
+      to: docs/internal/pipeline-stages.md
+      type: references
+    - from: docs/internal/pipeline-stages/tooling-pipeline.md
+      to: docs/internal/pipeline-stages.md
+      type: references
+    - from: docs/internal/pipeline-stages/bootstrap-pipeline.md
+      to: docs/internal/pipeline-stages.md
+      type: references
+    - from: docs/internal/protocol-tools.md
+      to: docs/internal/feature-registry.yaml
+      type: depends_on
+    - from: docs/internal/protocol-tools.md
+      to: docs/internal/gate-protocol.md
+      type: references
+    - from: docs/internal/protocol-tools.md
+      to: docs/internal/pipeline-stages.md
+      type: references
+    - from: docs/internal/protocol-tools.md
+      to: docs/internal/protocol-tools/tool-1-compliance.md
+      type: depends_on
+    - from: docs/internal/protocol-tools.md
+      to: docs/internal/protocol-tools/tool-2-drift.md
+      type: depends_on
+    - from: docs/internal/protocol-tools.md
+      to: docs/internal/protocol-tools/tool-3-workflow.md
+      type: depends_on
+    - from: docs/internal/protocol-tools.md
+      to: docs/internal/protocol-tools/tool-4-telemetry.md
+      type: depends_on
+    - from: docs/internal/protocol-tools.md
+      to: docs/internal/protocol-tools/tool-5-capability.md
+      type: depends_on
+    - from: docs/internal/protocol-tools.md
+      to: docs/internal/protocol-tools/cross-tool-integration.md
+      type: depends_on
+    - from: docs/internal/protocol-tools/cross-tool-integration.md
+      to: docs/internal/protocol-tools.md
+      type: references
+    - from: docs/internal/doc-update-policy.md
+      to: docs/internal/doc-tokens.yaml
+      type: depends_on
+    - from: docs/internal/rendered-examples-methodology.md
+      to: docs/guides/rendered-examples/state-example.md
+      type: references
+    - from: docs/internal/feature-domain-map.md
+      to: docs/internal/feature-registry.yaml
+      type: depends_on
+    - from: docs/internal/docs-navigation-agent.md
+      to: docs/workflow/interaction-patterns.md
+      type: references
+    - from: docs/internal/docs-navigation-agent.md
+      to: docs/architecture/scoping-rules.md
+      type: references
+    - from: docs/internal/docs-navigation-agent.md
+      to: docs/architecture/dependency-cascade.md
+      type: references
+    - from: docs/internal/docs-navigation-agent.md
+      to: docs/architecture/file-roles.md
+      type: references
+    - from: docs/internal/docs-navigation-agent.md
+      to: docs/guides/for-developers.md
+      type: references