Using System Archaeologist

System Archaeologist - Codebase Architecture Analysis

Overview

Analyze existing codebases through coordinated subagent exploration to produce comprehensive architecture documentation with C4 diagrams, subsystem catalogs, and architectural assessments.

Core principle: Systematic archaeological process with quality gates prevents rushed, incomplete analysis.

Context Conservation (CRITICAL)

You are a COORDINATOR, not an analyst. Your primary context is precious - preserve it for orchestration decisions, not detailed code reading.

The Delegation Imperative

What You DO (Coordinator):

• Create workspace and coordination plan
• Make orchestration decisions (parallel vs sequential)
• Spawn subagents with clear task specifications
• Read subagent outputs (summaries, not raw files)
• Make proceed/revise decisions based on validation
• Synthesize final deliverables from subagent work

What You DO NOT Do (Delegate Instead):

• Read implementation files directly (subagent reads, you get summary)
• Perform detailed pattern analysis (spawn specialist)
• Write catalog entries yourself (spawn codebase-explorer)
• Validate your own work (spawn analysis-validator)
• Generate diagrams from scratch (spawn diagram agent)

Rationalization Blockers

When to Use

• User requests architecture documentation for existing codebase
• Need to understand unfamiliar system architecture
• Creating design docs for legacy systems
• Analyzing codebases of any size (small to large)
• User mentions: "analyze codebase", "architecture documentation", "system design", "generate diagrams"

How to Access Reference Sheets

IMPORTANT: All reference sheets are located in the SAME DIRECTORY as this SKILL.md file.

When this skill is loaded from: skills/using-system-archaeologist/SKILL.md

Reference sheets like analyzing-unknown-codebases.md are at: skills/using-system-archaeologist/analyzing-unknown-codebases.md

NOT at: skills/analyzing-unknown-codebases.md ← WRONG PATH

Mandatory Workflow

Step 1: Create Workspace (NON-NEGOTIABLE)

Before any analysis:

mkdir -p docs/arch-analysis-$(date +%Y-%m-%d-%H%M)/temp

Why this is mandatory:

• Organizes all analysis artifacts in one location
• Enables subagent handoffs via shared documents
• Provides audit trail of decisions
• Prevents file scatter across project

Common rationalization: "This feels like overhead when I'm pressured"

Reality: 10 seconds to create workspace saves hours of file hunting and context loss.

Step 1.5: Offer Deliverable Menu (MANDATORY)

After workspace creation, present deliverable options using AskUserQuestion tool.

See deliverable-options.md for the complete menu (Options A-G).

Key options:

• A) Full Analysis - Comprehensive documentation
• B) Quick Overview - Fast turnaround, documented limitations
• C) Architect-Ready - Full analysis + improvement planning
• E) Full + Security - Security surface mapping included
• F) Full + Quality - Test infrastructure + dependency analysis
• G) Comprehensive - Everything

Common rationalization: "User didn't specify, so I'll default to full analysis"

Reality: Always offer choice explicitly. Different needs require different outputs.

Step 2: Write Coordination Plan

After documenting deliverable choice, write 00-coordination.md:

## Analysis Plan
- Scope: [directories to analyze]
- Strategy: [Sequential/Parallel with reasoning]
- Time constraint: [if any, with scoping plan]
- Complexity estimate: [Low/Medium/High]

## Execution Log
- [timestamp] Created workspace
- [timestamp] [Next action]

Common rationalization: "I'll just do the work, documentation is overhead"

Reality: Undocumented work is unreviewable and non-reproducible.

Step 3: Holistic Assessment First

Before diving into details, perform systematic scan:

1. Directory structure - Map organization (feature? layer? domain?)
2. Entry points - Find main files, API definitions, config
3. Technology stack - Languages, frameworks, dependencies
4. Subsystem identification - Identify 4-12 major cohesive groups

Write findings to 01-discovery-findings.md

Common rationalization: "I can see the structure, no need to document it formally"

Reality: What's obvious to you now is forgotten in 30 minutes.

Step 4: Subagent Orchestration Strategy

Decision point: Sequential vs Parallel vs Ultralarge per-module track

Use SEQUENTIAL when:

• Project < 5 subsystems
• Subsystems have tight interdependencies
• Quick analysis needed (< 1 hour)

Use PARALLEL when:

• Project ≥ 5 independent subsystems
• Large codebase (20K–100K LOC, 10+ plugins/services)
• Subsystems are loosely coupled

Use ULTRALARGE PER-MODULE TRACK when ANY of:

• Source LOC > 100,000
• Subsystem candidates > 12
• Test corpus LOC ≥ source LOC
• Doc corpus > 500 markdown files
• Plugin-registry architecture with extensible categories

The ultralarge track abandons single-pass orchestration and switches to manual subsystem partitioning + per-module review-with-scribe. Use the /analyze-ultralarge command, not /analyze-codebase. See:

• Tier criteria & partitioning protocol → partitioning-ultralarge-repos.md
• Per-module loop → module-by-module-with-scribe.md
• Findings schema (load-bearing) → findings-schema.md

Common rationalization: "Solo work is faster than coordination overhead"

Reality: For large systems, orchestration overhead (5 min) saves hours of sequential work. For ultralarge systems, single-pass orchestration produces a thin, sample-driven catalog that misses entire subsystems — the per-module track is non-negotiable at that scale.

Step 5: Subagent Delegation Pattern

When spawning subagents for analysis:

Create task specification in temp/task-[subagent-name].md:

## Task: Analyze [specific scope]
## Context
- Workspace: docs/arch-analysis-YYYY-MM-DD-HHMM/
- Read: 01-discovery-findings.md
- Write to: 02-subsystem-catalog.md (append your section)

## Expected Output
Follow contract in documentation-contracts.md:
- Subsystem name, location, responsibility
- Key components (3-5 files/classes)
- Dependencies (inbound/outbound)
- Patterns observed
- Confidence level

## Validation Criteria
- [ ] All contract sections complete
- [ ] Confidence level marked
- [ ] Dependencies bidirectional (if A depends on B, B shows A as inbound)

Step 6: Validation Gates (MANDATORY)

After EVERY major document is produced, validate before proceeding.

SPAWN VALIDATION SUBAGENT (Required for ≥3 subsystems)

• Spawn dedicated validation subagent using Task tool
• Agent reads document + contract, produces validation report
• Write validation report to temp/validation-[document].md

Self-validation ONLY permitted when ALL conditions met:

1. Single-subsystem analysis (1-2 subsystems only)
2. Total analysis time < 30 minutes
3. YOU personally did ALL the work (no subagents involved)
4. AND you document validation EVIDENCE (not just checkmarks)

If ANY condition is not met → SPAWN VALIDATION SUBAGENT. No exceptions.

Validation Rationalization Blockers

Validation Status Meanings

• APPROVED → Proceed to next phase
• NEEDS_REVISION (warnings) → Fix non-critical issues, document as tech debt, proceed
• NEEDS_REVISION (critical) → BLOCK. Fix issues, re-validate. Max 2 retries, then escalate to user.

Step 7: Handle Validation Failures

When validator returns NEEDS_REVISION with CRITICAL issues:

1. Read validation report (temp/validation-*.md)
2. Identify specific issues (not general "improve quality")
3. Spawn original subagent again with fix instructions
4. Re-validate after fix
5. Maximum 2 retries - if still failing, escalate to user

DO NOT:

• Proceed to next phase despite BLOCK status
• Make fixes yourself without re-spawning subagent
• Rationalize "it's good enough"
• Question validator authority

Working Under Pressure

Time Constraints Are Not Excuses to Skip Process

WRONG response: Skip workspace, skip validation, rush deliverables

RIGHT response: Scope appropriately while maintaining process

Example scoping for 3-hour deadline:

## Coordination Plan
- Time constraint: 3 hours until stakeholder presentation
- Strategy: SCOPED ANALYSIS with quality gates maintained
- Timeline:
  - 0:00-0:05: Create workspace, write coordination plan
  - 0:05-0:35: Holistic scan, identify all subsystems
  - 0:35-2:05: Focus on 3 highest-value subsystems (parallel analysis)
  - 2:05-2:35: Generate minimal viable diagrams (Context + Component only)
  - 2:35-2:50: Validate outputs
  - 2:50-3:00: Write executive summary with EXPLICIT limitations section

## Limitations Acknowledged
- Only 3/14 subsystems analyzed in depth
- No module-level dependency diagrams
- Confidence: Medium (time-constrained analysis)
- Recommend: Full analysis post-presentation

Key principle: Scoped analysis with documented limitations > complete analysis done wrong.

Resuming Prior Work (Sunk-Cost Discipline)

Common scenario: "We started this analysis last week, finish it."

Prior work is a hypothesis, not a foundation. Validate before continuing.

Checklist:

1. Find existing workspace - Look in docs/arch-analysis-*/.
2. Read the coordination log (00-coordination.md) - Understand what was done, what remains, and why work stopped.
3. Assess quality - Is the prior catalog/diagram/report contract-compliant? Are confidence levels documented? Were validation gates passed?
4. Make an EXPLICIT continue/archive/salvage decision:
   • Continue - Prior work passes contract + validation. Resume from the last checkpoint. Update coordination log.
   • Archive - Prior work is structurally flawed (wrong scope, wrong contract, no validation). Archive the old workspace (mv docs/arch-analysis-OLD docs/arch-analysis-OLD.archived-$(date +%Y-%m-%d)), start fresh, document why.
   • Salvage - Mixed quality. Keep good artifacts (e.g., discovery findings), redo bad ones (e.g., un-validated catalog). Document salvage decisions in the new coordination log.
5. For incremental analysis on a moving codebase (prior analysis was complete but the code has since changed), use the delta-analysis path - see incremental-analysis.md.

DO NOT assume prior work is correct just because it exists. DO NOT silently continue without recording a decision.

Coordination log entry:

## Resume Decision - [timestamp]
- Detected existing workspace: docs/arch-analysis-2026-05-15-1430/
- Last completed step: 02-subsystem-catalog.md (validated APPROVED)
- Assessment: Catalog contract-compliant, 11/14 subsystems analyzed
- Decision: SALVAGE - keep catalog, redo diagrams (3 missing subsystems), continue from Step 7
- Reasoning: Validator approved catalog; diagrams were skipped at original session end

Extreme Pressure Handling

If user requests something genuinely impossible (e.g., "Complete 15-plugin analysis in 1 hour"):

Provide scoped alternatives:

A) Quick overview (1 hour): Holistic scan, plugin inventory, high-level diagram B) Focused deep-dive (1 hour): Pick 2-3 critical plugins, full analysis of those C) Use existing docs (15 min): Synthesize existing README.md, CLAUDE.md D) Reschedule (recommended): Full analysis takes 4-6 hours for this scale

DO NOT refuse entirely. Provide realistic scoped alternatives.

Common Rationalizations (RED FLAGS)

If you catch yourself thinking ANY of these, STOP:

Specialist Subagent Integration

For complex codebases, leverage specialist subagents from other skillpacks.

See specialist-integration.md for:

• When to invoke specialists (by codebase type)
• Spawning pattern and output integration
• Cross-pack handoff points
• Technical accuracy escalation

Workflow Summary

1. Create workspace (docs/arch-analysis-YYYY-MM-DD-HHMM/)
1.5. Offer deliverable menu (A/B/C/D/E/F/G) - user chooses scope
2. Write coordination plan (00-coordination.md) with deliverable choice
3. Holistic assessment → 01-discovery-findings.md
4. Decide: Sequential or Parallel? (document reasoning)
5. Spawn subagents for analysis → 02-subsystem-catalog.md
6. VALIDATE subsystem catalog (mandatory gate)
6.5. (Optional) Code quality assessment → 05-quality-assessment.md
6.6. (Optional) Security surface mapping → 07-security-surface.md
6.7. (Optional) Test infrastructure analysis → 09-test-infrastructure.md
6.8. (Optional) Dependency analysis → 10-dependency-analysis.md
7. Spawn diagram generation → 03-diagrams.md
8. VALIDATE diagrams (mandatory gate)
9. Synthesize final report → 04-final-report.md
10. VALIDATE final report (mandatory gate)
11. (Optional) Generate architect handover → 06-architect-handover.md
12. Provide cleanup recommendations for temp/

Every step is mandatory except optional steps (6.5-6.8, 11). No exceptions.

Success Criteria

You have succeeded when:

• Workspace structure exists with all numbered documents
• Coordination log documents all major decisions
• All outputs passed validation gates
• Subagent orchestration used appropriately for scale
• Limitations explicitly documented if time-constrained

You have failed when:

• Files scattered outside workspace
• No coordination log showing decisions
• Validation skipped "to save time"
• Self-validated multi-subsystem work instead of spawning validator
• Worked solo despite clear parallelization opportunity
• Produced rushed outputs without limitation documentation

Anti-Patterns

❌ Skip workspace creation "I'll just write files to project root"

❌ No coordination logging "I'll just do the work without documenting strategy"

❌ Work solo despite scale "Orchestration overhead isn't worth it"

❌ Skip validation subagent "I already reviewed it myself" / "I'll do systematic self-validation"

❌ Self-validate multi-subsystem work "Time constraints mean self-validation is acceptable" (NO - spawn validator)

❌ Bypass BLOCK status "The validation is too strict, I'll proceed anyway"

❌ Complete refusal under pressure "I can't do this properly in 3 hours, so I won't do it" (Should: Provide scoped alternative)

Documentation Contracts

See individual skill files for detailed contracts:

• 01-discovery-findings.md contract → analyzing-unknown-codebases.md
• 02-subsystem-catalog.md contract → analyzing-unknown-codebases.md
• 03-diagrams.md contract → generating-architecture-diagrams.md
• 04-final-report.md contract → documenting-system-architecture.md
• 05-quality-assessment.md contract → assessing-code-quality.md
• 06-architect-handover.md contract → creating-architect-handover.md
• 07-security-surface.md contract → mapping-security-surface.md
• 08-incremental-report.md contract → incremental-analysis.md
• 09-test-infrastructure.md contract → analyzing-test-infrastructure.md
• 10-dependency-analysis.md contract → analyzing-dependencies.md
• Validation protocol → validating-architecture-analysis.md
• Language/framework patterns → language-framework-patterns.md
• Deliverable options → deliverable-options.md
• Specialist integration → specialist-integration.md
• Ultralarge tier criteria & partitioning → partitioning-ultralarge-repos.md
• Ultralarge per-module loop → module-by-module-with-scribe.md
• Ultralarge findings schema (load-bearing) → findings-schema.md