specification-refiner

name	specification-refiner
description	> Use when this capability is needed.

Specification Refiner

Systematically analyze and refine specifications, requirements, and architectural designs through iterative gap analysis with persistent memory, sequential clarification, and explicit user confirmation at each phase.

Core Workflow

0. ASSESS     → Evaluate complexity, select mode, confirm with user
1. INGEST     → Load document, confirm understanding with user
2. ANALYZE    → Run SEAMS + Critical Path, build coverage map
3. CLARIFY    → Sequential questions (one at a time), immediate integration
4. PRESENT    → Surface detailed findings, manage remaining questions
5. ITERATE    → Accept changes, re-analyze, present deltas
6. SYNTHESIZE → Present comprehensive summary for user approval
7. OUTPUT     → Generate refined specification(s) in Draft status
8. VALIDATE   → Review, validate traceability, advance status

Each phase ends with a full summary gate requiring user confirmation before proceeding.

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Standards Integration

This skill integrates with knowledge-mcp to ground analysis in engineering standards (IEEE, ISO, INCOSE).

Auto-Query Behavior

During Phase 2 (ANALYZE), the skill automatically queries knowledge-mcp for relevant standards:

1. Before SEAMS Analysis: Query "requirements engineering best practices [domain]"
2. Before Critical Path: Query "dependency analysis systems engineering"
3. For each finding: Query specific topics to validate against standards

Inline citations appear in findings:

"Per ISO/IEC/IEEE 12207:2017, Clause 6.4.2, requirements SHALL include verification criteria."

MCP Availability Check

Before querying, check MCP availability:

• If knowledge_search tool available: proceed with standards lookup
• If unavailable: warn user and continue without standards context

Never hallucinate citations. If MCP unavailable, state clearly:

"Note: Knowledge base unavailable. Analysis proceeds without standards context."

Graceful Degradation

If knowledge-mcp fails mid-analysis:

1. Log the failure
2. Continue analysis without standards
3. Note in findings: "Standards citation unavailable for this finding"

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Manual Commands

/lookup-standard

Query the knowledge base for specific standards information.

Syntax: /lookup-standard [natural language query]

Examples:

• /lookup-standard what does ISO say about traceability
• /lookup-standard IEEE 15288 verification methods
• /lookup-standard INCOSE requirements attributes

Response Format:

## Standards Lookup: [query]

### Result 1 (87% relevant)
**Source**: ISO/IEC/IEEE 12207:2017, Clause 6.4.2, p.23

[Content excerpt]

### Result 2 (74% relevant)
**Source**: INCOSE SE Handbook, Section 4.2, pp.45-47

[Content excerpt]

---
Showing 5 of 12 results. Say "show more" for additional results.

No Results:

No direct matches found for "[query]". Did you mean: [suggested related topics]?

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Phase 0: ASSESS

On receiving a specification document, first assess complexity to determine the appropriate mode.

Complexity Assessment

Evaluate these factors:

• Document size: Page/word count
• Domains identified: Single vs. multi-domain
• Stakeholder count: How many perspectives involved
• Scope clarity: Clear, moderate, or ambiguous boundaries

Mode Selection

Present to user:

Based on initial assessment:
- Document size: [X pages / Y words]
- Domains identified: [list domains]
- Stakeholder count: [N stakeholders]
- Scope clarity: [Clear/Moderate/Ambiguous]

Recommended mode: [SIMPLE/COMPLEX]

Options:
1. Proceed with recommended mode
2. Override to SIMPLE mode
3. Override to COMPLEX mode
4. Explain the modes in more detail

Your choice:

SIMPLE Mode: Single-domain, <10 pages, clear scope

• SEAMS analysis only
• Single A-Spec output with numbered requirements (A-REQ-NNN)

COMPLEX Mode: Multi-domain, >10 pages, ambiguous scope

• Full dual-framework analysis (SEAMS + Critical Path)
• A-Spec/B-Spec hierarchy per domain (see references/spec-hierarchy.md)
• Requirements Traceability Matrix generation

Phase 0 Gate

Present gate summary (see references/gate-templates.md for full format). Wait for user confirmation before proceeding.

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Phase 1: INGEST

Actions

1. Parse document structure (sections, dependencies, interfaces)
2. Create initial memory file: analysis-state.md using template from assets/analysis-state-template.md
3. Record mode selection in memory file
4. Identify document type and select appropriate analysis lenses
5. Note any questions that arise during parsing

Question Management

• Add questions to the Open Questions list with "Raised In: Phase 1: INGEST"
• Attempt to answer any Phase 0 questions from document content
• Update question statuses

Phase 1 Gate

Present full summary including: document info, sections identified, key entities, dependencies, and question status. See references/gate-templates.md for format. Wait for user confirmation—user may answer questions here.

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Phase 2: ANALYZE

Run analysis frameworks based on mode AND build the coverage map for clarification.

Standards Integration: Before beginning analysis, check if knowledge_search tool is available. If available, automatically query relevant standards during analysis to ground findings in engineering best practices.

SIMPLE Mode

Run SEAMS Analysis only (see references/seams-framework.md).

Auto-query pattern:

1. Before SEAMS: Query "requirements engineering best practices [domain]"
2. For each lens finding: Query specific topics for standards validation
3. Include inline citations in findings when relevant standards found

COMPLEX Mode

Run BOTH frameworks in parallel:

Framework A: SEAMS Analysis

Structure → Execution → Assumptions → Mismatches → Stakeholders

Auto-query before SEAMS: Query "requirements engineering best practices [domain]"

Lens	Questions to Answer
Structure	Completeness of I/O paths? Cohesion? Coupling risks? Boundary clarity?
Execution	Happy path works? Edge cases covered? Failure modes handled?
Assumptions	Technical assumptions? Organizational? Environmental?
Mismatches	Requirements ↔ Design aligned? Design ↔ Implementation consistent?
Stakeholders	Operator view? Security view? Integrator view? End-user view?

For each finding: Query relevant standards topic to validate and cite authoritative sources. Include inline citations in finding descriptions when standards support the observation.

Framework B: Critical Path Analysis

See references/critical-path-analysis.md for detailed methods.

Auto-query before Critical Path: Query "dependency analysis systems engineering"

1. Dependency Mapping: Build N² matrix
2. Critical Path Identification: Find longest/riskiest chains
3. Single Points of Failure: Cascade risk components
4. Bottleneck Detection: Throughput limiters
5. Temporal Analysis: Sequencing issues

For each critical finding: Query standards for validation and citation.

Coverage Map Generation

CRITICAL: Build a structured coverage map using the 11-category taxonomy:

Category	Status	Gap Count	Impact
Functional Scope & Behavior	[Clear/Partial/Missing]	[N]	[High/Med/Low]
Domain & Data Model	[Clear/Partial/Missing]	[N]	[High/Med/Low]
Interaction & UX Flow	[Clear/Partial/Missing]	[N]	[High/Med/Low]
Non-Functional Quality Attributes	[Clear/Partial/Missing]	[N]	[High/Med/Low]
Integration & External Dependencies	[Clear/Partial/Missing]	[N]	[High/Med/Low]
Edge Cases & Failure Handling	[Clear/Partial/Missing]	[N]	[High/Med/Low]
Constraints & Tradeoffs	[Clear/Partial/Missing]	[N]	[High/Med/Low]
Terminology & Consistency	[Clear/Partial/Missing]	[N]	[High/Med/Low]
Completion Signals	[Clear/Partial/Missing]	[N]	[High/Med/Low]
Assumptions & Risks	[Clear/Partial/Missing]	[N]	[High/Med/Low]
Misc & Placeholders	[Clear/Partial/Missing]	[N]	[High/Med/Low]

This map drives the CLARIFY phase question prioritization.

Phase 2 Gate

Present preliminary findings summary with severity counts, coverage map summary, top 3 issues, and blocked findings. Prompt to proceed to CLARIFY phase. See references/gate-templates.md for format.

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Phase 3: CLARIFY

CRITICAL: This phase uses SEQUENTIAL QUESTIONING to reduce cognitive load and enable immediate integration.

Clarification Principles

1. One question at a time - Never present multiple questions
2. Constrained answers - Multiple choice (2-5 options) OR short phrase (≤5 words)
3. Recommended answer - Always analyze and recommend the best option
4. Immediate integration - Update spec/analysis-state AFTER EACH answer
5. Maximum 5 questions - Per clarification session
6. Maximum 10 questions - Across entire analysis (including ITERATE loops)

Question Prioritization

Generate prioritized queue using Impact × Uncertainty scoring:

1. Score each potential question:

   • Impact: How much does this affect architecture, data model, task decomposition, test design, UX, ops readiness, or compliance? (1-5)
   • Uncertainty: How ambiguous is the current state? (1-5)
   • Priority Score = Impact × Uncertainty

2. Apply constraints:

   • Only include questions whose answers materially change implementation or validation
   • Ensure category balance (don't ask 3 questions from same category)
   • Exclude already-answered questions
   • Exclude trivial stylistic preferences
   • Favor questions that reduce downstream rework risk

3. Select top 5 by priority score

Question Format: Multiple Choice

When discrete options exist, present as:

### CLARIFY-001 [CATEGORY]

[Context: What triggered this question]

**Question**: [The specific question]

**Recommended:** Option [X] - [1-2 sentence reasoning based on best practices, risk reduction, or project context]

| Option | Description |
|--------|-------------|
| A | [Option A description] |
| B | [Option B description] |
| C | [Option C description] |
| D | [Option D description] (if needed) |
| Short | Provide a different short answer (≤5 words) |

Reply with the option letter (e.g., "A"), accept the recommendation by saying "yes" or "recommended", or provide your own short answer.

Question Format: Short Answer

When no meaningful discrete options exist:

### CLARIFY-001 [CATEGORY]

[Context: What triggered this question]

**Question**: [The specific question]

**Suggested:** [Your proposed answer] - [Brief reasoning]

Format: Short answer (≤5 words). You can accept the suggestion by saying "yes" or "suggested", or provide your own answer.

Answer Processing

1. If user replies "yes", "recommended", or "suggested": Use the stated recommendation/suggestion
2. If user provides option letter: Map to that option
3. If user provides custom answer: Validate it fits ≤5 word constraint
4. If ambiguous: Ask for quick disambiguation (doesn't count as new question)

Immediate Integration Protocol

AFTER EACH accepted answer (not at end of phase):

1. Create Clarifications section (if first answer this session):

   ## Clarifications
   
   ### Session YYYY-MM-DD
   - Q: [question] → A: [final answer]
   

2. Apply to appropriate section(s):

   Answer Type	Update Location
   Functional ambiguity	Functional Requirements section
   User interaction/actor	User Stories or Actors subsection
   Data shape/entities	Data Model section (fields, types, relationships)
   Non-functional constraint	Quality Attributes section (convert vague → metric)
   Edge case/negative flow	Edge Cases / Error Handling section
   Terminology conflict	Normalize term across entire spec

3. Handle conflicts:

   • If clarification invalidates earlier statement, REPLACE it (don't duplicate)
   • Leave no obsolete contradictory text

4. Save immediately: Atomic write after each integration

5. Update analysis-state.md: Log question as answered

Early Termination

Stop asking questions when:

• All critical ambiguities resolved (remaining questions unnecessary)
• User signals completion ("done", "good", "no more", "proceed")
• 5 questions reached in this session
• 10 total questions reached across analysis

No Questions Scenario

If no valid questions exist (full coverage), immediately report:

No critical ambiguities detected requiring formal clarification.
All categories show Clear status.
Recommend proceeding to Phase 4 (PRESENT).

Phase 3 Gate

Present clarification summary:

PHASE 3 COMPLETE: CLARIFICATION

Questions asked this session: [N]
Total questions asked (all phases): [M]

COVERAGE UPDATE:
| Category | Before | After | Notes |
|----------|--------|-------|-------|
| Functional Scope | Partial | Clear | Q1 resolved |
| Data Model | Missing | Clear | Q2, Q3 resolved |
| Edge Cases | Partial | Partial | Deferred (low impact) |
...

Clarifications integrated:
1. [Q1]: [Answer] → Updated [Section]
2. [Q2]: [Answer] → Updated [Section]
...

DEFERRED TO LATER:
- [Category]: [Reason - e.g., better suited for planning phase]

OUTSTANDING (low impact):
- [Category]: [Why not addressed - e.g., exceeds question quota]

Options:
1. Proceed to Phase 4 (PRESENT) with findings
2. Run another clarification session (if quota allows)
3. Review updated specification sections

Your choice:

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Phase 4: PRESENT

Finding Format

For EACH identified issue, include: ID, title, category, severity, confidence, blocked-by status, description, evidence, impact, remediation options (with trade-offs), and related issues. See references/gate-templates.md for full template.

Presentation Order

Present findings grouped by:

1. Critical blockers (must fix before proceeding)
2. Significant gaps (high impact, clear remediation)
3. Optimization opportunities (efficiency improvements)
4. Considerations (context-dependent, need user input)

Question Management

• Present all unanswered questions explicitly
• Ask user to answer questions or confirm assumptions
• Update question tracking with answers received

Phase 4 Gate

Present findings summary with severity counts, question status, and assumptions made. Offer options: (1) Iterate, (2) Skip to Synthesize, (3) Run more clarification, (4) Review details. See references/gate-templates.md for format.

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Phase 5: ITERATE

When user provides new information, constraints, or requests changes:

Actions

1. Validate new input against existing analysis
2. Identify affected areas in the specification
3. Re-run analysis on affected sections only (delta analysis)
4. Update coverage map based on new information
5. Assess cascading effects on previously-identified issues
6. Update memory file with new state

Triggering Additional Clarification

If iteration reveals new ambiguities:

• Check if question quota allows (10 total max)
• If yes, offer to run additional CLARIFY session
• If no, note as deferred with reason

Question Management

• Add new questions with "Raised In: Phase 5: ITERATE"
• Check if new input answers existing questions
• Update all question statuses

Phase 5 Gate

Present delta summary: changes incorporated, coverage map update, new/modified/resolved findings, key changes, question status. Offer options: (1) Continue iterating, (2) Synthesize, (3) Run clarification, (4) Review findings. See references/gate-templates.md for format.

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Phase 6: SYNTHESIZE

Before generating any output, present a comprehensive summary for user approval.

Summary Contents

Present comprehensive summary covering:

• Document Overview: Title, mode, iteration count, clarification count
• Coverage Summary: Final coverage map with all categories
• Findings Resolution: By severity with resolved/unresolved breakdown, key resolutions, unresolved critical/high items
• Clarifications Applied: All Q&A with section updates
• Questions Status: Answered, unanswered (with impact), deferred (with reason)
• Assumptions: Confirmed vs. unverified
• Proposed Output Structure: Based on mode (single doc for SIMPLE, separate files for COMPLEX)

See references/gate-templates.md for full format.

Phase 6 Gate

Offer options: (1) Approve and output, (2) Return to iterate, (3) Modify structure, (4) Answer questions. Wait for explicit approval before generating output.

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Phase 7: OUTPUT

Generate refined specification(s) based on mode, all in Draft status.

SIMPLE Mode Output

Generate single A-Spec document (refined-specification.md) with:

• Numbered requirements (A-REQ-001, A-REQ-002, etc.)
• All resolved findings incorporated
• Selected remediations applied
• Clarifications section with session log
• Documented assumptions
• Remaining open questions in dedicated section

COMPLEX Mode Output

Generate specification hierarchy per domain:

A-Spec files (one per domain):

• Naming: [domain]-a-spec.md
• Requirements: A-REQ-[DOMAIN]-NNN
• High-level requirements defining WHAT

B-Spec files (one or more per domain):

• Naming: [domain]-[subsystem]-b-spec.md
• Requirements: B-REQ-[DOMAIN]-NNN
• Each requirement MUST include Traces to: A-REQ-XXX-NNN
• Detailed requirements defining HOW

Supporting files:

• traceability-matrix.md - Full RTM (see assets/traceability-matrix-template.md)
• clarifications-log.md - All clarification sessions
• cross-cutting-concerns.md (if applicable)
• open-items.md

See references/spec-hierarchy.md for detailed format specifications.

RTM Generation (COMPLEX mode)

1. Extract all A-REQ-* from A-Spec files
2. Extract all B-REQ-* from B-Spec files with their traces
3. Build coverage matrix
4. Calculate coverage percentage
5. Identify gaps (A-Reqs with no B-Req coverage)
6. Generate traceability-matrix.md
7. Update analysis-state.md with RTM summary

Final Actions

1. Set all specification statuses to Draft
2. Update analysis-state.md with completion status and RTM summary
3. Present output files to user
4. Summarize what was generated
5. Prompt transition to Phase 8

Phase 7 Completion

Present: mode, files created with requirement counts, RTM summary (COMPLEX mode), findings addressed, clarifications integrated, assumptions documented. Prompt user to proceed to Phase 8. See references/gate-templates.md for format.

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Phase 8: VALIDATE

Final review and validation phase ensuring specifications are comprehensive, traceable, and approved. Mandatory for both SIMPLE and COMPLEX modes.

Status Workflow

Specifications progress through statuses:

Draft → Reviewed → Approved → Baselined

• Draft: Initial output from Phase 7 (automatic)
• Reviewed: Technical review complete, no critical gaps
• Approved: Stakeholder sign-off received
• Baselined: Locked for change control

Validation Actions

1. Completeness check: All required sections present, cross-references valid
2. RTM validation (COMPLEX): Coverage percentage, gap identification
3. Traceability check (COMPLEX): All B-Reqs trace to A-Reqs
4. Consistency check: Terminology, formatting, priority scales aligned
5. Clarification integration check: All answers properly incorporated
6. Present validation findings with severity

Status Advancement

• Require explicit user approval to advance status
• Document status change with timestamp and approver
• Update analysis-state.md with new status and history

Advancement Criteria

Transition	Requirements
Draft → Reviewed	No critical RTM gaps, completeness checks pass
Reviewed → Approved	All high-priority issues resolved, stakeholder review
Approved → Baselined	Formal approval documented, change control established

Phase 8 Gate

Present validation summary with:

• Current status and proposed advancement
• RTM coverage metrics (COMPLEX mode)
• Completeness and consistency checklist
• Clarification integration verification
• Validation findings
• Options: advance status, return to fix issues, review details

See references/gate-templates.md for full template.

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Ambiguity Taxonomy (11 Categories)

1. Functional Scope & Behavior

• Core user goals & success criteria
• Explicit out-of-scope declarations
• User roles / personas differentiation

2. Domain & Data Model

• Entities, attributes, relationships
• Identity & uniqueness rules
• Lifecycle/state transitions
• Data volume / scale assumptions

3. Interaction & UX Flow

• Critical user journeys / sequences
• Error/empty/loading states
• Accessibility or localization notes

4. Non-Functional Quality Attributes

• Performance (latency, throughput targets)
• Scalability (horizontal/vertical, limits)
• Reliability & availability (uptime, recovery)
• Observability (logging, metrics, tracing)
• Security & privacy (authN/Z, data protection)
• Compliance / regulatory constraints

5. Integration & External Dependencies

• External services/APIs and failure modes
• Data import/export formats
• Protocol/versioning assumptions

6. Edge Cases & Failure Handling

• Negative scenarios
• Rate limiting / throttling
• Conflict resolution (e.g., concurrent edits)

7. Constraints & Tradeoffs

• Technical constraints (language, storage, hosting)
• Explicit tradeoffs or rejected alternatives

8. Terminology & Consistency

• Canonical glossary terms
• Avoided synonyms / deprecated terms

9. Completion Signals

• Acceptance criteria testability
• Measurable Definition of Done indicators

10. Assumptions & Risks

• Technical assumptions (infrastructure, dependencies)
• Organizational assumptions (skills, process)
• Environmental assumptions (security, compliance)

11. Misc & Placeholders

• TODO markers / unresolved decisions
• Ambiguous adjectives ("robust", "intuitive") lacking quantification

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Question Tracking System

Question Categories (Expanded)

Map to the 11-category taxonomy for better coverage tracking.

Question Lifecycle

1. Raised: Question identified, logged with phase and category
2. Queued: Selected for clarification, prioritized by Impact × Uncertainty
3. Asked: Presented to user in sequential flow
4. Answered: Response received and validated
5. Integrated: Applied to specification with atomic write
6. Deferred: Explicitly set aside with reason and revisit trigger

Question Table Format

Track questions in analysis-state.md using tables:

Unanswered:

ID	Question	Category	Raised In	Priority Score	Blocks

Answered:

ID	Question	Answer	Category	Asked In	Integrated To

Deferred:

ID	Question	Category	Reason	Deferred In	Revisit When

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Memory File Management

Required Memory File: analysis-state.md

Use the template from assets/analysis-state-template.md. Key sections:

• Document metadata (title, version, hash)
• Mode selection (SIMPLE/COMPLEX)
• Coverage map (11 categories)
• Analysis iterations table
• Clarification sessions log
• Active and resolved findings
• Question tracking tables (per-phase)
• Assumption register
• User-provided constraints

Update Protocol

After EACH phase AND after EACH clarification answer:

1. Read current analysis-state.md
2. Update phase completion status
3. Update coverage map
4. Update finding statuses
5. Update question tables
6. Record new assumptions
7. Log user decisions
8. Write updated file (atomic)

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Analysis Depth Calibration

Match depth to document maturity:

Document Stage	Analysis Focus
Concept/Idea	Feasibility, scope clarity, key assumptions
Draft Spec	Completeness, internal consistency, missing sections
Detailed Design	Interface contracts, error handling, edge cases
Implementation Plan	Dependencies, sequencing, resource conflicts
Review/Audit	Full SEAMS sweep, stakeholder perspectives

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Quick Assessment Mode

For rapid feedback when full analysis is not needed:

1. Boundaries: What's in/out of scope?
2. One Thread: Trace critical path from input to output
3. Three Assumptions: The riskiest unstated beliefs
4. Silent Failure: What breaks without notice?
5. Naive Question: What would a newcomer ask that has no answer?

Note: Quick Assessment skips the full phase gate workflow but still creates analysis-state.md.

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Output Formatting

Severity Indicators

• 🔴 Critical: Blocks progress, must address
• 🟠 High: Significant risk, should address soon
• 🟡 Medium: Notable issue, plan to address
• 🟢 Low: Minor concern, address opportunistically

Confidence Qualifiers

• High confidence: Clear evidence, well-understood domain
• Medium confidence: Reasonable inference, some ambiguity
• Low confidence: Pattern recognition, needs validation

Coverage Status Indicators

• ✅ Clear: Sufficient information, no clarification needed
• ⚠️ Partial: Some gaps, may need clarification
• ❌ Missing: Critical gaps, clarification required

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Handling Incomplete Information

When specifications are incomplete:

1. Note the gap explicitly with category
2. Score Impact × Uncertainty for prioritization
3. Add to clarification queue if score warrants
4. State what would be needed to complete analysis
5. Offer reasonable assumptions (clearly marked)
6. Add question to tracking system
7. Document in assumption register

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Anti-Patterns to Avoid

• Vague criticism without specific evidence
• Recommendations without trade-off analysis
• Analysis paralysis on minor issues
• Ignoring stated constraints to suggest "ideal" solutions
• Failing to update memory after iterations
• Treating all findings as equal severity
• Proceeding past a gate without user confirmation
• Losing track of open questions
• Generating output without synthesis approval
• Generating B-Specs without traces to A-Specs
• Skipping RTM generation for COMPLEX mode
• Advancing status without validation
• Baselining specs with unresolved critical gaps
• Presenting multiple questions at once during CLARIFY
• Failing to recommend an answer
• Delaying integration until end of CLARIFY phase
• Exceeding question limits (5 per session, 10 total)

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