agent-method 1.5.3 → 1.5.6

package/templates/entry-points/CLAUDE.md

@@ -7,7 +7,8 @@
 
 1. This file is auto-loaded — read it first
 2. Read `STATE.md` for current position, decisions, blockers
-3. Scope based on query type (see table below)
+3. Check `PROJECT-PROFILE.md` for lifecycle stage and active extensions
+4. Scope based on query type (see table below)
 
 ## Scoping rules
 
@@ -15,10 +16,16 @@
 |------------|-------------------|-------------------|
 | **Planning / roadmap** | REQUIREMENTS.md, ROADMAP.md | STATE.md, PLAN.md |
 | **Context refresh** | .context/ (all), project structure | .context/, this file (if scoping rules affected) |
+| **Project discovery** | Project structure, package files, key source files | .context/BASE.md, .context/ specialists, STATE.md |
 | **{your-domain-type}** | .context/BASE.md + .context/{SPECIALIST}.md | {affected working files} |
+| **Structural navigation** | .context/REGISTRY.md | .context/REGISTRY.md (if structure changed) |
 | **Methodology guidance** | .context/METHODOLOGY.md | -- |
 | **Phase completion** | SUMMARY.md | SUMMARY.md, STATE.md, ROADMAP.md |
 | **Backlog / ideas** | todos/backlog.md | todos/backlog.md |
+| **Management overview** | Management/DIGEST.md, Management/STATUS.md, STATE.md | Management/STATUS.md, Management/DIGEST.md |
+| **Project review** | Reviews/INDEX.md, relevant source files | Reviews/ (affected review file) |
+| **Workflow analysis** | agentWorkflows/INDEX.md, SESSION-LOG.md | agentWorkflows/ (affected analysis file) |
+| **Docs update** | .context/DOCS-MAP.md, relevant docs/ files | docs/ files, .context/DOCS-MAP.md |
 
 <!-- INSTRUCTION: Replace the {your-domain-type} row with project-specific query types.
      Each should pair .context/BASE.md with one specialist. Add as many rows as needed. -->
@@ -35,18 +42,129 @@ When a file changes, check this table and update dependent files in the same res
 | Open question resolved | STATE.md (mark resolved with resolution text, don't delete) |
 | Project structure | .context/BASE.md (codebase map), this file (if new query types needed) |
 | Intelligence layer file exceeds 300 lines | Restructure into index + components subdirectory (keep active content, archive completed sections) |
+| File split, created, deleted, or renamed | .context/REGISTRY.md (file tree, topic index, structural log) |
 | New domain area | .context/BASE.md, consider new .context/ specialist, this file (if new scoping row) |
-| Session close or high-effort task completion | SESSION-LOG.md (append metrics entry — effort, ambiguity, context level, tokens, time, workflow, features, cascades, friction, findings) |
+| Lifecycle stage change | PROJECT-PROFILE.md (update stage + date), STATE.md (record decision) |
+| Session close or high-effort task completion | SESSION-LOG.md (append metrics entry — effort, ambiguity, context level, tokens, time, user response, refinement delta, workflow, features, cascades, friction, findings). For high-effort tasks also: Management/DIGEST.md (append row — date, task, query, outcome, key changes, decisions, effort, time), Management/STATUS.md (if milestone) |
+| Significant milestone or phase completion | Management/STATUS.md (update current state, recent decisions, health indicators) |
+| New project component or module | .context/DOCS-MAP.md (add component mapping, check scaffolding rules for new docs/ proposals) |
+| docs/ file created or deleted | .context/DOCS-MAP.md (update inventory), docs/index.md (update navigation — create if it doesn't exist yet) |
 
 <!-- INSTRUCTION: Add project-specific cascade rules below the universal ones above. -->
 
+## Docs maintenance
+
+<!-- INSTRUCTION: This table tells the agent when to update human-facing docs.
+     For full component-to-docs mapping, see .context/DOCS-MAP.md. -->
+
+| Trigger | Update these docs/ files |
+|---------|------------------------|
+| Phase completed | docs/index.md (progress section — create from DOCS-MAP.md if it doesn't exist yet) |
+| Architecture decision | docs/index.md (architecture section), .context/DOCS-MAP.md (if new component) |
+| New project component | .context/DOCS-MAP.md (add mapping), docs/ (per DOCS-MAP.md scaffolding rules) |
+| {structural-change} | {specific docs/ files per DOCS-MAP.md component mapping} |
+
 ## Workflow
 
 Select based on query type:
 - **General task** — Review, Plan, Implement, Document, Update
 - **Code change** — Review, Plan, Implement, Context-sync, Update
 - **Context refresh** — Scan, Compare, Update-context, Cascade, Record
-- **First session** — Detect, Initialize, Map, Pair, Ready
+- **First session (greenfield)** — Ask, Populate, Confirm (see onboarding protocol below)
+- **First session (brownfield)** — Scan, Ask, Confirm (see onboarding protocol below)
+
+## First session protocol
+
+<!-- AGENT: Follow this protocol on the FIRST session when methodology files contain only template placeholders. -->
+
+When PROJECT.md still contains `{placeholder}` text, this is a first session. Guide the user through onboarding — ask questions, show what you'll write, get confirmation before writing each file.
+
+### Greenfield onboarding (no existing codebase)
+
+**Stage 1 — Project vision** → populates PROJECT.md
+Ask the user:
+1. What is your project about? (1-2 sentences)
+2. Who is it for?
+3. What problem does it solve?
+4. What technologies, languages, or frameworks will you use?
+5. What are 2-3 guiding principles for this project?
+
+CHECKPOINT: Draft PROJECT.md from the answers. Show the user the draft. Wait for approval before writing.
+
+**Stage 2 — Architecture** → populates .context/BASE.md, PROJECT-PROFILE.md, .context/DOCS-MAP.md
+Ask the user:
+1. What are the main components or modules?
+2. How do they connect? (data flow, API calls, event-driven, etc.)
+3. What is the directory structure? (or what will it be?)
+4. What are the key dependencies?
+
+CHECKPOINT: Draft .context/BASE.md, PROJECT-PROFILE.md, and .context/DOCS-MAP.md (initial component-to-docs mapping based on architecture). Show the user. Wait for approval.
+
+**Stage 3 — Goals** → populates ROADMAP.md, PLAN.md
+Ask the user:
+1. What are your immediate goals? (next 1-3 sessions)
+2. What does "done" look like for this project?
+3. Can you break this into 2-4 phases?
+
+CHECKPOINT: Draft ROADMAP.md and PLAN.md (first task). Show the user. Wait for approval.
+
+**Stage 4 — Starting state** → populates STATE.md
+Ask the user:
+1. Any decisions already made? (tech choices, architecture, constraints)
+2. Any known blockers or risks?
+3. Any open questions you want tracked?
+
+CHECKPOINT: Draft STATE.md. Show the user. Wait for approval. Then begin normal work.
+
+### Brownfield onboarding (existing codebase)
+
+**Stage 1 — Scan** → reads existing files, writes nothing
+Read: package.json, README, directory structure, key config files, entry points.
+Present findings: "Here's what I found in your project: [summary]. Is this accurate?"
+
+CHECKPOINT: Wait for user to confirm or correct your understanding.
+
+**Stage 2 — Clarify** → populates PROJECT.md, PROJECT-PROFILE.md
+Ask targeted questions based on what the scan missed:
+1. What's the intent behind [pattern you found]?
+2. Are there conventions not captured in config? (naming, structure, etc.)
+3. What's the current state — active development, maintenance, exploration?
+
+CHECKPOINT: Draft PROJECT.md from scan + answers. Show the user. Wait for approval.
+
+**Stage 3 — Map** → populates .context/BASE.md, .context/DOCS-MAP.md
+Build codebase map from scan. Ask:
+1. Are there areas of the codebase I should understand deeply vs. ignore?
+2. Any architectural decisions I should know about that aren't documented?
+3. What are the most common types of changes you make?
+
+CHECKPOINT: Draft .context/BASE.md and .context/DOCS-MAP.md (component-to-docs mapping from scan results). Show the user. Wait for approval.
+
+**Stage 4 — Organize** → proposes entry point customization
+Based on understanding, propose:
+1. Scoping rules — which query types match this project?
+2. Specialist context files — which domains need their own .context/ file?
+3. Cascade rules — what project-specific dependencies exist?
+
+CHECKPOINT: Show proposed entry point customizations. Wait for approval before modifying this file.
+
+**Stage 5 — Starting state** → populates STATE.md, ROADMAP.md
+Propose initial state based on everything learned:
+1. Decisions already implicit in the codebase (document them)
+2. Current position (where is the project in its lifecycle?)
+3. Immediate goals
+
+CHECKPOINT: Draft STATE.md and ROADMAP.md. Show the user. Wait for approval. Then begin normal work.
+
+### Checkpoint rules
+
+- NEVER write to a methodology file without showing the user what you will write first
+- At each CHECKPOINT, present the draft as a code block the user can review
+- If the user says "looks good" or similar, write the file
+- If the user edits or corrects, incorporate changes and show the updated draft
+- If the user says "skip", leave the file as template placeholder
+- After all stages complete, summarize what was populated and begin normal work
+- For brownfield: `.context/REGISTRY.md` is deferred — do not create it during onboarding. It will be created automatically when the first file split occurs (reduces first-session cognitive load)
 
 ## Interaction level
 
@@ -56,7 +174,7 @@ mode: checkpoint
 
 ## Model tier
 
-tier: standard
+tier: full
 <!-- lite | standard | full -->
 <!-- lite: minimal rules, STATE.md only, 2 cascade rules — for Haiku or simple projects -->
 <!-- standard: core rules + context pairing, overflow to .context/METHODOLOGY.md — for Sonnet (default) -->
@@ -66,21 +184,28 @@ tier: standard
 
 method_version: 1.5
 <!-- Tracks which methodology version generated this entry point -->
-<!-- Use `npx wwa status` to compare against latest -->
+<!-- Use `wwa status` to compare against latest -->
 
 ## CLI tools (optional)
 
-Available via `npx wwa` (zero-install) or `pip install wwa-tools`:
+Install: `npm install -g agent-method` (then use `wwa`), or `pip install wwa-tools`.
 
 | When you want to... | Run |
 |---------------------|-----|
-| Validate this entry point | `npx wwa check` |
-| See what type of project this is | `npx wwa scan` |
-| Test how a query routes | `npx wwa route "your question"` |
-| Extract a refinement report | `npx wwa refine` |
-| Check methodology version | `npx wwa status` |
-| Update methodology files | `npx wwa upgrade` |
-| See what an entry point should contain | `npx wwa init code` / `context` / `data` / `mix` |
+| Validate this entry point | `wwa check` |
+| See what type of project this is | `wwa scan` |
+| Test how a query routes | `wwa route "your question"` |
+| See current plan status | `wwa plan` |
+| Get implementation guidance | `wwa implement` |
+| View project review dashboard | `wwa review` |
+| Show management digest | `wwa digest` |
+| Session close + project snapshot | `wwa close` |
+| Extract a refinement report | `wwa refine` |
+| Extract a case study (with project tokens) | `wwa casestudy` |
+| Check docs coverage | `wwa docs` |
+| Check methodology version | `wwa status` |
+| Update methodology files | `wwa upgrade` |
+| Set up a new project | `wwa init code` / `context` / `data` / `mix` |
 
 <!-- INSTRUCTION: The agent can suggest these commands when the user asks about validation,
      project setup, or methodology updates. All commands auto-detect project type and find
@@ -95,7 +220,9 @@ Available via `npx wwa` (zero-install) or `pip install wwa-tools`:
 - Surface uncertainty as open questions in STATE.md — never guess silently
 - Keep intelligence layer files under 300 lines — split into index + components subdirectory when exceeded
 - Propose plans and wait for approval — the human controls direction
-- At session close or after any high-effort task, append a metrics entry to SESSION-LOG.md — include effort level, question ambiguity, context level, estimated tokens, and time. Never skip, never read previous entries during normal work
+- Document proportionally — low-effort tasks (status checks, lookups, clarifications) need no STATE.md or SESSION-LOG updates; high-effort tasks get full recording
+- SUMMARY.md is the session audit trail (date, plan, outcome, files, decisions, next). Management digest lives in Management/DIGEST.md
+- At session close or after any high-effort task, append a metrics entry to SESSION-LOG.md — include effort level, question ambiguity, context level, estimated tokens, time, user response (accepted/edited/revised/rejected/redirected), and for medium/high effort tasks: revision count, refinement magnitude (none/minor/moderate/major/rework), delta categories, and survival rate. Never skip, never read previous entries during normal work
 
 ## Do not
 
@@ -105,5 +232,7 @@ Available via `npx wwa` (zero-install) or `pip install wwa-tools`:
 - Defer STATE.md decision recording to end of session
 - Skip cascade checks after file changes
 - Load multiple specialist .context/ files for a single query
+- Update docs/ for typo fixes or internal-only changes
+- Record routine queries in STATE.md or SESSION-LOG.md — only decisions, blockers, and high-effort work warrant documentation
 
 <!-- INSTRUCTION: Add project-specific "do not" rules as you discover common mistakes -->

package/templates/extensions/analytical-system.md

@@ -11,7 +11,7 @@
      5. Add the conventions and do-not items to your existing lists
      6. Delete this file after merging — it's a reference, not a runtime file
 
-     Derived from: feature-registry.yaml (v1.4) query_patterns [analytical] + WF-06
+     Derived from: feature-registry.yaml (v1.5) query_patterns [analytical] + WF-06
      Specialists referenced: COMPOSITION.md, EVALUATION.md, EXECUTION.md, DOMAIN.md, UI_CONTEXT.md
      Key difference: analytical systems iterate — compose, evaluate, refine cycles are the norm
 -->

package/templates/extensions/code-project.md

@@ -11,7 +11,7 @@
      5. Add the conventions and do-not items to your existing lists
      6. Delete this file after merging — it's a reference, not a runtime file
 
-     Derived from: feature-registry.yaml (v1.1) query_patterns [code] + WF-02
+     Derived from: feature-registry.yaml (v1.5) query_patterns [code] + WF-02
      Specialists referenced: customize the specialist names to match your project
 -->
 

package/templates/extensions/data-exploration.md

@@ -11,7 +11,7 @@
      5. Add the conventions and do-not items to your existing lists
      6. Delete this file after merging — it's a reference, not a runtime file
 
-     Derived from: feature-registry.yaml (v1.1) query_patterns [data] + WF-05
+     Derived from: feature-registry.yaml (v1.5) query_patterns [data] + WF-05
      Specialists referenced: SCHEMA.md, DOCUMENTS.md, RELATIONSHIPS.md
      Key difference: most exploration queries are READ-ONLY — no file changes, no cascades
 -->

package/templates/full/.context/BASE.md

@@ -66,3 +66,36 @@
 | PROJECT.md | Project vision and structure |
 | REQUIREMENTS.md | What must be achieved, with phase traceability |
 | SUMMARY.md | Execution history — session audit trail |
+
+## Agent onboarding
+
+<!-- AGENT: Use these questions to populate this file during the first session.
+     Ask the user each question at Stage 2 (Architecture), draft this file from
+     the answers, and show the draft at the checkpoint before writing.
+     Remove this section after the file is populated — it's scaffolding. -->
+
+### Greenfield
+
+Ask the user:
+1. What are the main components or modules? (populate "What this system is")
+2. How do they connect? Data flow, API calls, event-driven? (populate System model)
+3. What is the directory structure and what does each directory do? (populate Codebase map)
+4. What are the key external dependencies? (populate Dependencies table)
+5. What recurring task types will you work on? (populate Pairing protocol — helps create specialist context files)
+
+### Brownfield
+
+<!-- AGENT: For brownfield projects, auto-populate most of this from the Stage 1 scan.
+     Build the codebase map from what you found. Ask targeted questions only for gaps. -->
+
+Pre-fill from scan:
+- **What this system is**: infer from README + source structure + config files
+- **System model**: infer from imports, API routes, database connections, event patterns
+- **Codebase map**: build from directory listing + language detection + framework patterns
+- **Dependencies**: extract from lockfiles and config
+
+Ask the user only for gaps:
+1. I found [components]. Are there connections between them I'm missing? (validate System model)
+2. Which parts of the codebase get the most changes? (helps prioritize Pairing protocol)
+3. Are there historical patterns or conventions not visible in code? (e.g., "we always use X for Y")
+4. What types of work will you primarily do? (populate Pairing protocol for specialist files)

package/templates/full/.context/METHODOLOGY.md

@@ -11,8 +11,33 @@ Select based on query type:
 - **General task** — Review, Plan, Implement, Document, Update
 - **Code change** — Review, Plan, Implement, Context-sync, Update
 - **Context refresh** — Scan, Compare, Update-context, Cascade, Record
-- **First session** — Detect, Initialize, Map, Pair, Ready
-- **Discovery (brownfield)** — Inventory, Map-dependencies, Extract-patterns, Assess, Bootstrap
+- **First session (greenfield)** — Ask, Populate, Confirm (see entry point onboarding protocol)
+- **First session (brownfield)** — Scan, Ask, Confirm (see entry point onboarding protocol)
+
+## Checkpoint protocol
+
+The first session protocol in the entry point defines stage-by-stage checkpoints for onboarding. These rules apply to all checkpoints, both during onboarding and normal work:
+
+### When to checkpoint
+
+- **Onboarding**: After each stage's questions are answered, before writing any file
+- **Normal work**: Before executing any plan (checkpoint interaction level)
+- **File writes**: Never write methodology files without showing a preview first
+
+### Checkpoint format
+
+1. Present the draft as a code block the user can review
+2. Wait for explicit approval ("looks good", "yes", "approved")
+3. If the user edits or corrects, incorporate changes and show updated draft
+4. If the user says "skip", leave the file as template placeholder
+
+### Brownfield safeguards
+
+- Stage 1 (Scan) reads only — no writes under any circumstances
+- Existing project files are never modified — methodology files only
+- Entry point customizations are proposed, not applied, until approved
+- Agent presents scan findings as questions, not assertions
+- `.context/REGISTRY.md` is deferred — not created during onboarding (created on first file split to reduce cognitive load on smaller models)
 
 ## Interaction level
 
@@ -56,9 +81,41 @@ When any intelligence layer file exceeds 300 lines (~3,750 tokens):
 3. Components hold archived sections grouped by semantic boundary
 4. Update .context/REGISTRY.md (if it exists) with new file entries
 
-## Audit trail format
+## Reporting layers
+
+Three directories separate reporting concerns from operational files:
+
+### Management/
+
+Management-facing project oversight. Managers read this, not STATE.md or SESSION-LOG.md.
+
+- **DIGEST.md** — Append a row for every high-effort task. Format: date, task, query, outcome, key changes, decisions, effort, time. Low-effort work is NOT recorded.
+- **STATUS.md** — Update after milestones: current phase, active work, recent decisions (last 5), blockers, health indicators.
+
+**What qualifies as high-effort**: Multi-file changes (3+ files), architectural decisions, phase completions, complex multi-step queries, new feature implementations.
+
+**What does NOT qualify**: Status checks, lookups, clarifications, single-file bug fixes, routine maintenance, configuration changes.
+
+### Reviews/
+
+Synthesized views of intelligence layer files. Updated when doing a "project review" query.
+
+- **INDEX.md** — Dashboard with key metrics and links to drill-down files.
+- **Drill-down files**: roadmap.md, plan.md, project.md, requirements.md, state.md, backlog.md — each synthesizes from its source file.
+- Update the corresponding review file when source data changes significantly, not on every edit.
+
+### agentWorkflows/
+
+Agent workflow performance analysis. Updated after high-effort sessions.
+
+- **INDEX.md** — Workflow summary, quick stats, links to analysis files.
+- **sessions.md** — SESSION-LOG.md synthesis: effort distribution, query patterns, acceptance rates, refinement analysis.
+- **patterns.md** — Extracted behavioral patterns: what works, friction points, anti-patterns, improvement suggestions.
+- **observations.md** — Case study observations: findings with methodology implications, severity classification, refinement candidates.
+
+### Audit trail format
 
-SUMMARY.md session entries follow this structure:
+SUMMARY.md is the session audit trail. Each entry follows this structure:
 ```
 ### {date} — {brief description}
 **Plan**: {what was planned}
@@ -73,7 +130,7 @@ SUMMARY.md session entries follow this structure:
 
 | Trigger | Update these docs/ files |
 |---------|------------------------|
-| Phase completed | docs/index.md (progress section) |
+| Phase completed | docs/index.md (progress section — create from DOCS-MAP.md if it doesn't exist yet) |
 | Architecture decision | docs/index.md (architecture section) |
 
 ## Navigation registry protocol

package/templates/full/.cursorrules

@@ -22,6 +22,10 @@
 | **Methodology guidance** | .context/METHODOLOGY.md | -- |
 | **Phase completion** | SUMMARY.md | SUMMARY.md, STATE.md, ROADMAP.md |
 | **Backlog / ideas** | todos/backlog.md | todos/backlog.md |
+| **Management overview** | Management/DIGEST.md, Management/STATUS.md, STATE.md | Management/STATUS.md, Management/DIGEST.md |
+| **Project review** | Reviews/INDEX.md, relevant source files | Reviews/ (affected review file) |
+| **Workflow analysis** | agentWorkflows/INDEX.md, SESSION-LOG.md | agentWorkflows/ (affected analysis file) |
+| **Docs update** | .context/DOCS-MAP.md, relevant docs/ files | docs/ files, .context/DOCS-MAP.md |
 
 <!-- INSTRUCTION: Replace the {your-domain-type} row with project-specific query types.
      Each should pair .context/BASE.md with one specialist. Add as many rows as needed. -->
@@ -41,20 +45,24 @@ When a file changes, check this table and update dependent files in the same res
 | File split, created, deleted, or renamed | .context/REGISTRY.md (file tree, topic index, structural log) |
 | New domain area | .context/BASE.md, consider new .context/ specialist, this file (if new scoping row) |
 | Lifecycle stage change | PROJECT-PROFILE.md (update stage + date), STATE.md (record decision) |
-| Session close or high-effort task completion | SESSION-LOG.md (append metrics entry — effort, ambiguity, context level, tokens, time, workflow, features, cascades, friction, findings) |
+| Session close or high-effort task completion | SESSION-LOG.md (append metrics entry — effort, ambiguity, context level, tokens, time, user response, refinement delta, workflow, features, cascades, friction, findings). For high-effort tasks also: Management/DIGEST.md (append row — date, task, query, outcome, key changes, decisions, effort, time), Management/STATUS.md (if milestone) |
+| Significant milestone or phase completion | Management/STATUS.md (update current state, recent decisions, health indicators) |
+| New project component or module | .context/DOCS-MAP.md (add component mapping, check scaffolding rules for new docs/ proposals) |
+| docs/ file created or deleted | .context/DOCS-MAP.md (update inventory), docs/index.md (update navigation — create if it doesn't exist yet) |
 
 <!-- INSTRUCTION: Add project-specific cascade rules below the universal ones above. -->
 
 ## Docs maintenance
 
 <!-- INSTRUCTION: This table tells the agent when to update human-facing docs.
-     Add rows as your docs/ structure grows. -->
+     For full component-to-docs mapping, see .context/DOCS-MAP.md. -->
 
 | Trigger | Update these docs/ files |
 |---------|------------------------|
-| Phase completed | docs/index.md (progress section) |
-| Architecture decision | docs/index.md (architecture section) |
-| {structural-change} | {specific docs/ files} |
+| Phase completed | docs/index.md (progress section — create from DOCS-MAP.md if it doesn't exist yet) |
+| Architecture decision | docs/index.md (architecture section), .context/DOCS-MAP.md (if new component) |
+| New project component | .context/DOCS-MAP.md (add mapping), docs/ (per DOCS-MAP.md scaffolding rules) |
+| {structural-change} | {specific docs/ files per DOCS-MAP.md component mapping} |
 
 ## Workflow
 
@@ -62,8 +70,101 @@ Select based on query type:
 - **General task** — Review, Plan, Implement, Document, Update
 - **Code change** — Review, Plan, Implement, Context-sync, Update
 - **Context refresh** — Scan, Compare, Update-context, Cascade, Record
-- **First session** — Detect, Initialize, Map, Pair, Ready
-- **Discovery (brownfield)** — Inventory, Map-dependencies, Extract-patterns, Assess, Bootstrap
+- **First session (greenfield)** — Ask, Populate, Confirm (see onboarding protocol below)
+- **First session (brownfield)** — Scan, Ask, Confirm (see onboarding protocol below)
+
+## First session protocol
+
+<!-- AGENT: Follow this protocol on the FIRST session when methodology files contain only template placeholders. -->
+
+When PROJECT.md still contains `{placeholder}` text, this is a first session. Guide the user through onboarding — ask questions, show what you'll write, get confirmation before writing each file.
+
+### Greenfield onboarding (no existing codebase)
+
+**Stage 1 — Project vision** → populates PROJECT.md
+Ask the user:
+1. What is your project about? (1-2 sentences)
+2. Who is it for?
+3. What problem does it solve?
+4. What technologies, languages, or frameworks will you use?
+5. What are 2-3 guiding principles for this project?
+
+CHECKPOINT: Draft PROJECT.md from the answers. Show the user the draft. Wait for approval before writing.
+
+**Stage 2 — Architecture** → populates .context/BASE.md, PROJECT-PROFILE.md, .context/DOCS-MAP.md
+Ask the user:
+1. What are the main components or modules?
+2. How do they connect? (data flow, API calls, event-driven, etc.)
+3. What is the directory structure? (or what will it be?)
+4. What are the key dependencies?
+
+CHECKPOINT: Draft .context/BASE.md, PROJECT-PROFILE.md, and .context/DOCS-MAP.md (initial component-to-docs mapping based on architecture). Show the user. Wait for approval.
+
+**Stage 3 — Goals** → populates ROADMAP.md, PLAN.md
+Ask the user:
+1. What are your immediate goals? (next 1-3 sessions)
+2. What does "done" look like for this project?
+3. Can you break this into 2-4 phases?
+
+CHECKPOINT: Draft ROADMAP.md and PLAN.md (first task). Show the user. Wait for approval.
+
+**Stage 4 — Starting state** → populates STATE.md
+Ask the user:
+1. Any decisions already made? (tech choices, architecture, constraints)
+2. Any known blockers or risks?
+3. Any open questions you want tracked?
+
+CHECKPOINT: Draft STATE.md. Show the user. Wait for approval. Then begin normal work.
+
+### Brownfield onboarding (existing codebase)
+
+**Stage 1 — Scan** → reads existing files, writes nothing
+Read: package.json, README, directory structure, key config files, entry points.
+Present findings: "Here's what I found in your project: [summary]. Is this accurate?"
+
+CHECKPOINT: Wait for user to confirm or correct your understanding.
+
+**Stage 2 — Clarify** → populates PROJECT.md, PROJECT-PROFILE.md
+Ask targeted questions based on what the scan missed:
+1. What's the intent behind [pattern you found]?
+2. Are there conventions not captured in config? (naming, structure, etc.)
+3. What's the current state — active development, maintenance, exploration?
+
+CHECKPOINT: Draft PROJECT.md from scan + answers. Show the user. Wait for approval.
+
+**Stage 3 — Map** → populates .context/BASE.md, .context/DOCS-MAP.md
+Build codebase map from scan. Ask:
+1. Are there areas of the codebase I should understand deeply vs. ignore?
+2. Any architectural decisions I should know about that aren't documented?
+3. What are the most common types of changes you make?
+
+CHECKPOINT: Draft .context/BASE.md and .context/DOCS-MAP.md (component-to-docs mapping from scan results). Show the user. Wait for approval.
+
+**Stage 4 — Organize** → proposes entry point customization
+Based on understanding, propose:
+1. Scoping rules — which query types match this project?
+2. Specialist context files — which domains need their own .context/ file?
+3. Cascade rules — what project-specific dependencies exist?
+
+CHECKPOINT: Show proposed entry point customizations. Wait for approval before modifying this file.
+
+**Stage 5 — Starting state** → populates STATE.md, ROADMAP.md
+Propose initial state based on everything learned:
+1. Decisions already implicit in the codebase (document them)
+2. Current position (where is the project in its lifecycle?)
+3. Immediate goals
+
+CHECKPOINT: Draft STATE.md and ROADMAP.md. Show the user. Wait for approval. Then begin normal work.
+
+### Checkpoint rules
+
+- NEVER write to a methodology file without showing the user what you will write first
+- At each CHECKPOINT, present the draft as a code block the user can review
+- If the user says "looks good" or similar, write the file
+- If the user edits or corrects, incorporate changes and show the updated draft
+- If the user says "skip", leave the file as template placeholder
+- After all stages complete, summarize what was populated and begin normal work
+- For brownfield: `.context/REGISTRY.md` is deferred — do not create it during onboarding. It will be created automatically when the first file split occurs (reduces first-session cognitive load)
 
 ## Interaction level
 
@@ -83,21 +184,28 @@ tier: full
 
 method_version: 1.5
 <!-- Tracks which methodology version generated this entry point -->
-<!-- Use `npx wwa status` to compare against latest -->
+<!-- Use `wwa status` to compare against latest -->
 
 ## CLI tools (optional)
 
-Available via `npx wwa` (zero-install) or `pip install wwa-tools`:
+Install: `npm install -g agent-method` (then use `wwa`), or `pip install wwa-tools`.
 
 | When you want to... | Run |
 |---------------------|-----|
-| Validate this entry point | `npx wwa check` |
-| See what type of project this is | `npx wwa scan` |
-| Test how a query routes | `npx wwa route "your question"` |
-| Extract a refinement report | `npx wwa refine` |
-| Check methodology version | `npx wwa status` |
-| Update methodology files | `npx wwa upgrade` |
-| See what an entry point should contain | `npx wwa init code` / `context` / `data` / `mix` |
+| Validate this entry point | `wwa check` |
+| See what type of project this is | `wwa scan` |
+| Test how a query routes | `wwa route "your question"` |
+| See current plan status | `wwa plan` |
+| Get implementation guidance | `wwa implement` |
+| View project review dashboard | `wwa review` |
+| Show management digest | `wwa digest` |
+| Session close + project snapshot | `wwa close` |
+| Extract a refinement report | `wwa refine` |
+| Extract a case study (with project tokens) | `wwa casestudy` |
+| Check docs coverage | `wwa docs` |
+| Check methodology version | `wwa status` |
+| Update methodology files | `wwa upgrade` |
+| Set up a new project | `wwa init code` / `context` / `data` / `mix` |
 
 <!-- INSTRUCTION: The agent can suggest these commands when the user asks about validation,
      project setup, or methodology updates. All commands auto-detect project type and find
@@ -112,8 +220,9 @@ Available via `npx wwa` (zero-install) or `pip install wwa-tools`:
 - Surface uncertainty as open questions in STATE.md — never guess silently
 - Keep intelligence layer files under 300 lines — split into index + components subdirectory when exceeded
 - Propose plans and wait for approval — the human controls direction
-- SUMMARY.md entries follow audit trail format: date, plan, outcome, files, decisions, next
-- At session close or after any high-effort task, append a metrics entry to SESSION-LOG.md — include effort level, question ambiguity, context level, estimated tokens, and time. Never skip, never read previous entries during normal work
+- Document proportionally — low-effort tasks (status checks, lookups, clarifications) need no STATE.md or SESSION-LOG updates; high-effort tasks get full recording
+- SUMMARY.md is the session audit trail (date, plan, outcome, files, decisions, next). Management digest lives in Management/DIGEST.md
+- At session close or after any high-effort task, append a metrics entry to SESSION-LOG.md — include effort level, question ambiguity, context level, estimated tokens, time, user response (accepted/edited/revised/rejected/redirected), and for medium/high effort tasks: revision count, refinement magnitude (none/minor/moderate/major/rework), delta categories, and survival rate. Never skip, never read previous entries during normal work
 
 ## Do not
 
@@ -124,5 +233,6 @@ Available via `npx wwa` (zero-install) or `pip install wwa-tools`:
 - Skip cascade checks after file changes
 - Load multiple specialist .context/ files for a single query
 - Update docs/ for typo fixes or internal-only changes
+- Record routine queries in STATE.md or SESSION-LOG.md — only decisions, blockers, and high-effort work warrant documentation
 
 <!-- INSTRUCTION: Add project-specific "do not" rules as you discover common mistakes -->