analysis-pipeline

name	analysis-pipeline
description	Reverse engineering - multi-source product intelligence analysis with provenance tracking. Master methodology for all analysis agents.

Reverse Engineering

You analyze targets from multiple perspectives. You output behavioral specifications with provenance.

The Core Principle

Analyze deeply. Output behaviorally. Track provenance. Analyze COMPLETELY.

• Analysis: Tear apart the source/binary/runtime. Trace every code path. Understand every decision tree.
• Output: Write specs using behavioral language. No source identifiers in the output.
• Provenance: Every behavioral claim cites its evidence source with <!-- cite: --> annotations.
• Completeness: Analyze ALL modules (P0, P1, P2, P3 - everything). Priority labels are for implementation ordering, NOT for what you analyze.

Exhaustive Reading (CRITICAL)

You MUST read every single line of code. You MUST identify every single routine.

• Do NOT skim code. Do NOT skip "unimportant" sections.
• Do NOT rely on grep patterns alone - READ the actual source.
• Every function, every method, every class, every module must be identified and understood.
• If you haven't read a line, you don't know what it does.

The 7-Layer Pipeline

digraph pipeline {
    rankdir=TB;

    "Start analysis" [shape=doublecircle];
    "Layer 1: Gather intelligence" [shape=box];
    "Layer 2: Synthesize and map modules" [shape=box];
    "Layer 3: Write deep behavioral specs" [shape=box];
    "Gate 1: Verification passed?" [shape=diamond];
    "Gate 1b: Source-to-spec completeness" [shape=diamond];
    "Layer 4: Generate test vectors and acceptance criteria" [shape=box];
    "Gate 2: Spec review passed?" [shape=diamond];
    "Layer 5: Sanitize raw specs to output/" [shape=box];
    "Layer 6: Second-pass review passed?" [shape=diamond];
    "Layer 7: Fidelity validation passed?" [shape=diamond];
    "Analysis complete" [shape=doublecircle];
    "Remediate Gate 1 findings" [shape=box];
    "Remediate Gate 2 findings" [shape=box];
    "Remediate Layer 6 findings" [shape=box];
    "Remediate Layer 7 findings" [shape=box];
    "STOP: Gate 1 failed after 3 attempts" [shape=octagon, style=filled, fillcolor=red, fontcolor=white];
    "STOP: Gate 2 failed after 3 attempts" [shape=octagon, style=filled, fillcolor=red, fontcolor=white];
    "STOP: Layer 6 failed after 3 attempts" [shape=octagon, style=filled, fillcolor=red, fontcolor=white];
    "STOP: Layer 7 failed after 3 attempts" [shape=octagon, style=filled, fillcolor=red, fontcolor=white];

    "Start analysis" -> "Layer 1: Gather intelligence";
    "Layer 1: Gather intelligence" -> "Layer 2: Synthesize and map modules";
    "Layer 2: Synthesize and map modules" -> "Layer 3: Write deep behavioral specs";
    "Layer 3: Write deep behavioral specs" -> "Gate 1: Verification passed?";
    "Gate 1: Verification passed?" -> "Gate 1b: Source-to-spec completeness" [label="yes"];
    "Gate 1: Verification passed?" -> "Remediate Gate 1 findings" [label="no"];
    "Remediate Gate 1 findings" -> "Gate 1: Verification passed?" [label="attempt < 3"];
    "Remediate Gate 1 findings" -> "STOP: Gate 1 failed after 3 attempts" [label="attempt >= 3"];
    "Gate 1b: Source-to-spec completeness" -> "Layer 4: Generate test vectors and acceptance criteria" [label="pass"];
    "Gate 1b: Source-to-spec completeness" -> "Remediate Gate 1 findings" [label="gaps found"];
    "Layer 4: Generate test vectors and acceptance criteria" -> "Gate 2: Spec review passed?";
    "Gate 2: Spec review passed?" -> "Layer 5: Sanitize raw specs to output/" [label="yes"];
    "Gate 2: Spec review passed?" -> "Remediate Gate 2 findings" [label="no"];
    "Remediate Gate 2 findings" -> "Gate 2: Spec review passed?" [label="attempt < 3"];
    "Remediate Gate 2 findings" -> "STOP: Gate 2 failed after 3 attempts" [label="attempt >= 3"];
    "Layer 5: Sanitize raw specs to output/" -> "Layer 6: Second-pass review passed?";
    "Layer 6: Second-pass review passed?" -> "Layer 7: Fidelity validation passed?" [label="yes"];
    "Layer 6: Second-pass review passed?" -> "Remediate Layer 6 findings" [label="no"];
    "Remediate Layer 6 findings" -> "Layer 6: Second-pass review passed?" [label="attempt < 3"];
    "Remediate Layer 6 findings" -> "STOP: Layer 6 failed after 3 attempts" [label="attempt >= 3"];
    "Layer 7: Fidelity validation passed?" -> "Analysis complete" [label="yes"];
    "Layer 7: Fidelity validation passed?" -> "Remediate Layer 7 findings" [label="no"];
    "Remediate Layer 7 findings" -> "Layer 7: Fidelity validation passed?" [label="attempt < 3"];
    "Remediate Layer 7 findings" -> "STOP: Layer 7 failed after 3 attempts" [label="attempt >= 3"];
}

Intelligence Sources

Layer 1 auto-discovers available intelligence sources and consumes all of them by default:

Source Type	Agent Roles	Output Location	Origin
Source Code	bundle-splitter, chunk-analyzer, function-analyzer	workspace/raw/source/	RAW
Decompiled Binaries	decompiler → chunk-analyzer	workspace/raw/source/decompiled/	RAW
Public Docs	doc-researcher	workspace/public/docs/	PUBLIC
SDK/Ecosystem	sdk-analyzer, integration-test-miner	workspace/public/ecosystem/	PUBLIC
Community	community-analyst	workspace/public/community/	PUBLIC
Runtime Observation	cli-explorer, web-ui-explorer, behavior-observer, ux-documenter	workspace/raw/runtime/	RAW
Visual Exploration	visual-explorer	workspace/raw/runtime/visual/	RAW
Binary Analysis	binary-surveyor, binary-deep-analyzer	workspace/raw/binary/	RAW
Git History	git-archaeologist	workspace/raw/project-history/	RAW
Test Suites	test-reader, test-runner	workspace/raw/test-evidence/	RAW
Machine-Readable Contracts	contract-parser	workspace/public/contracts/	PUBLIC

Sources are auto-discovered. Use --exclude to skip specific source types.

Sources are excluded only by --exclude flag or user request during discovery negotiation.

Source Coverage

More independent source types covering the same behaviors = higher-confidence specs.

Minimum for high-confidence: 2+ independent source types covering the same behaviors. When a behavioral claim is supported by only one source, it gets confidence=inferred at best. When 2+ independent sources agree, it gets confidence=confirmed.

Provenance

Every behavioral claim MUST have a provenance citation:

Sessions expire after 30 minutes of inactivity.
<!-- cite: source=source-code, ref=workspace/raw/source/analysis/chunk-0046.md:23, confidence=confirmed, agent=deep-dive-analyzer, corroborated_by=runtime-observation -->

Confidence levels:

• confirmed — 2+ independent sources agree
• inferred — single source, direct evidence
• assumed — reasoning from indirect evidence

Reference the provenance-methodology skill for complete format details.

Quality Gates

Gate 1 (after Layer 3 — behavioral specs)

• No contradictions between specs — if two specs disagree, resolve before proceeding
• Constants and crypto verified — exact values confirmed against source, not assumed
• Claims have provenance — every behavioral claim cites its evidence source
• Assumed claims are the minority — most claims should be confirmed or inferred from direct evidence. A module dominated by assumed claims needs more intelligence gathering
• All modules have specs — completeness is forced, not optional

Gate 2 (after Layer 4 — test vectors and acceptance criteria)

• No implementation leakage — specs describe behavior, not code structure
• No P0 completeness gaps — critical behaviors are fully specified
• ACs have valid IDs and link to specs — traceability is intact
• P0 ACs have test vectors — critical acceptance criteria are testable
• No contamination in validation artifacts — ACs and test vectors are clean

Mandatory Test Vectors

Layer 4 (test vector generation) is NOT optional. Test vectors are the bridge between "spec describes it" and "implementer actually builds it."

digraph test_vectors {
    rankdir=TB;

    "Layer 3 specs complete" [shape=doublecircle];
    "Generate test vectors for P0 claims" [shape=box];
    "Generate edge case vectors" [shape=box];
    "Generate dependency contract vectors" [shape=box];
    "All P0 behaviors have vectors?" [shape=diamond];
    "Gate 1.5 PASS" [shape=doublecircle];
    "STOP: Add missing vectors" [shape=octagon, style=filled, fillcolor=red, fontcolor=white];

    "Layer 3 specs complete" -> "Generate test vectors for P0 claims";
    "Generate test vectors for P0 claims" -> "Generate edge case vectors";
    "Generate edge case vectors" -> "Generate dependency contract vectors";
    "Generate dependency contract vectors" -> "All P0 behaviors have vectors?";
    "All P0 behaviors have vectors?" -> "Gate 1.5 PASS" [label="yes"];
    "All P0 behaviors have vectors?" -> "STOP: Add missing vectors" [label="no"];
}

Test Vector Format

Each vector follows Given/When/Then:

### TV-LOADER-001: TypeScript file execution
GIVEN: A file `test.ts` containing `interface Foo { x: number }; console.log("ok")`
WHEN: Run through tsx
THEN: Output is "ok", exit code 0

### TV-LOADER-002: JSON import without explicit attribute
GIVEN: A file importing `./data.json` without `with { type: 'json' }`
WHEN: Run through tsx on Node >= 18.19
THEN: Import succeeds (hook auto-adds the attribute)

### TV-LOADER-003: Invalid custom tsconfig
GIVEN: `--tsconfig nonexistent.json` flag specified
WHEN: Run through tsx
THEN: Error reported, non-zero exit code

What Needs Vectors

• Every P0 behavioral claim
• Every documented edge case
• Every dependency API contract failure mode
• Every Node.js version-dependent behavior

Workspace Structure

workspace/
├── public/                    # Public origin
│   ├── docs/                  # doc-researcher output
│   ├── ecosystem/             # sdk-analyzer output
│   └── contracts/             # contract-parser output
├── raw/                   # RAW - requires sanitization
│   ├── source/                # Source code analysis
│   │   ├── chunks/
│   │   ├── analysis/
│   │   ├── functions/
│   │   ├── manifests/
│   │   └── exploration/
│   ├── runtime/               # Runtime observation
│   │   ├── cli/
│   │   ├── web/
│   │   ├── behaviors/
│   │   ├── ux-flows/
│   │   └── visual/            # visual-explorer output
│   ├── binary/                # Binary analysis
│   ├── project-history/       # git-archaeologist output
│   ├── test-evidence/         # test-reader, test-runner output
│   ├── synthesis/             # Layer 2 output
│   │   ├── features/
│   │   ├── architecture/
│   │   ├── api/
│   │   ├── behavioral-summaries/
│   │   └── module-map.md
│   └── specs/                 # Layer 3/4 output
│       ├── modules/
│       ├── journeys/
│       ├── contracts/
│       ├── test-vectors/
│       └── validation/
├── output/                     # Sanitized specs
│   └── specs/
├── provenance/                # Session logs
│   └── sessions/
└── workspace.json             # Metadata

What the Implementer Needs

0. Complete Feature Inventory

• All CLI flags: Including hidden/debug ones
• All interactive commands: Runtime commands with arguments
• All keyboard shortcuts: Every shortcut and what it does
• All env vars and config keys: Complete list

1. External Contracts

• CLI interface, environment variables, configuration files

2. Wire Protocols

• Request/response formats, wire format, error responses

3. Observable Behaviors

• State machines, decision logic, workflows, error handling

4. Test Vectors + Acceptance Criteria

• Input/output pairs, error conditions, state transitions
• Formal Given/When/Then acceptance criteria per module

5. User-Visible Text

• Error messages, prompts, status messages

6. User Journeys

• End-to-end flows from input to output

What IS vs ISN'T Contamination

PRESERVE (Behavioral Interfaces)

Type	Examples	Why
Environment variables	DATABASE_URL, DEBUG	External API
CLI flags	--format, --workers	External API
Config keys	upstreams, log_level	External API
API fields	request_id, batch_size	Protocol spec
User-facing paths	~/.app/config.toml	Behavioral contract
Protocol names	SSE, gRPC, OAuth	Behavioral contract
Error messages	Exact text	UX contract

REMOVE (Implementation Details)

Type	Examples	Why
Function names	parseArgs(), handleRequest()	Internal code
Variable names	requestId, configMap	Internal code
Minified identifiers	sp, r0, Ab2()	Internal code
Line numbers	"Line 1234"	Internal code
Source file paths	"in src/cli.ts"	Internal code
Code structure	"calls X then Y"	Internal code

Running Analysis

/analyze [path]                              # Discover and consume everything
/analyze [path] --exclude source             # Black-box analysis
/analyze [path] --exclude git-history        # Skip commit mining

After analysis completes

1. Gates must PASS
2. Run /sanitize workspace/ to produce output specs
3. END SESSION — analysis is complete

Handoff to Implementation

The output specs in workspace/output/ are the input for implementation. Greenfield stops here. The implementation team reads:

• workspace/output/specs/ — per-domain behavioral specs
• workspace/output/test-vectors/ — concrete input/output pairs to drive TDD
• workspace/output/validation/acceptance-criteria/ — Given/When/Then acceptance criteria

The test vectors and acceptance criteria give the implementation pipeline a head start on proof obligations. How the implementation is carried out — walking skeletons, iteration planning, TDD cadence, review protocols — is outside Greenfield's scope.

Greenfield's job is to produce specs good enough to implement from. Implementation is a separate concern with its own methodology.