audit-context-building

name	audit-context-building
description	Ultra-granular code analysis for deep architectural context building. Line-by-line and block-by-block analysis using First Principles, 5 Whys, 5 Hows methodology at micro scale. Builds mental models, tracks invariants and assumptions, and maps cross-function call flows for security audit preparation.
version	1.2.0
model	sonnet
invoked_by	both
user_invocable	true
tools	["Read","Glob","Grep","Bash","Write"]
args	<target-path> [--depth deep|standard] [--focus security|architecture|correctness]
best_practices	["Always read code line-by-line before forming any conclusions","Track every assumption and invariant explicitly in notes","Build mental models incrementally from concrete code, never from abstractions","Map cross-function call flows completely before analyzing individual functions","Document what the code ACTUALLY does, not what comments say it does"]
error_handling	graceful
streaming	supported
agents	["security-architect","code-reviewer","developer"]
verified	true
lastVerifiedAt	"2026-03-01T00:00:00.000Z"
source	builtin
trust_score	100
provenance_sha	d501e2508e0a2fa2

Audit Context Building Skill

Ultra-granular code analysis skill adapted from Trail of Bits audit methodology. Builds deep architectural context through systematic line-by-line analysis using First Principles, 5 Whys, and 5 Hows at micro scale. Designed for security audit preparation, architectural understanding, and correctness verification. - Line-by-line and block-by-block code analysis - First Principles reasoning at code-level granularity - 5 Whys root cause analysis at micro scale - 5 Hows implementation verification at micro scale - Mental model building from concrete code paths - Invariant and assumption tracking across functions - Cross-function call flow mapping and analysis - State transition identification and verification - Trust boundary identification and classification - Data flow tracking through function boundaries - Anti-hallucination enforcement: conclusions from code only

Overview

This skill implements Trail of Bits' audit context building methodology for the agent-studio framework. The core principle is: never form conclusions about code without reading it line by line first. This skill systematically builds understanding from the ground up, tracking every assumption, invariant, and data flow explicitly.

Source repository: https://github.com/trailofbits/skills License: CC-BY-SA-4.0 Methodology: First Principles + 5 Whys + 5 Hows at micro scale

When to Use

• Before security audits to build deep codebase understanding
• When analyzing unfamiliar codebases for architectural review
• When debugging complex cross-function interactions
• When verifying correctness of critical code paths (auth, crypto, state machines)
• When preparing for threat modeling with concrete code evidence
• When onboarding to a new codebase section that handles sensitive operations

Iron Laws

1. NEVER form conclusions without line-by-line evidence — every claim about code behavior MUST be backed by specific line references; if you have not read the code, you do not know what it does.
2. NEVER trust comments over actual code — comments describe intent, code describes behavior; when they conflict, the code is authoritative; always verify what comments claim.
3. NEVER skip error handling paths — error paths frequently contain security-relevant behavior (fallback auth, leaked stack traces, privilege bypass) that is invisible to happy-path analysis.
4. ALWAYS map cross-function call flows before analyzing individual functions — isolated function analysis misses inter-function trust assumptions; understand the full call chain first.
5. ALWAYS record unverified assumptions explicitly — an unverified assumption is an unexamined risk; mark every assumption with [UNVERIFIED] and track it until confirmed or disproven.

Anti-Hallucination Rules

1. Never assume what a function does based on its name alone
2. Never trust comments over actual code behavior
3. Never skip error handling paths -- they often contain security-relevant behavior
4. Never extrapolate behavior from one code path to another without verification
5. Always note when you have NOT read a dependency and mark assumptions as unverified

Phase 1: Initial Reconnaissance

Goal: Map the surface area before diving deep.

Steps

1. Enumerate entry points: Find all public APIs, CLI commands, HTTP handlers, event listeners
2. Map the module graph: Identify imports, exports, and dependency relationships
3. Identify trust boundaries: Where does external input enter? Where do privilege changes occur?
4. Catalog data stores: Databases, files, caches, environment variables, secrets

Output Format

## Reconnaissance Report

### Entry Points

- [ ] `path/to/file.ts:42` - HTTP handler `POST /api/login`
- [ ] `path/to/file.ts:89` - HTTP handler `GET /api/users/:id`

### Trust Boundaries

- [ ] External input at: [list locations]
- [ ] Privilege escalation at: [list locations]
- [ ] Serialization/deserialization at: [list locations]

### Data Stores

- [ ] Database: [type, access patterns]
- [ ] File system: [paths, permissions]
- [ ] Environment: [variables accessed]

Phase 2: Deep Analysis (Line-by-Line)

Goal: Build precise mental model of each critical code path.

The Analysis Loop

For each function/method under analysis:

1. Read every line. No skipping.
2. For each line, ask:
   • What state does this line depend on?
   • What state does this line modify?
   • What can go wrong here? (error paths)
   • What assumptions does this line make about its inputs?
   • Is the assumption validated upstream?
3. Track in a structured note:

### Function: `authenticateUser(req, res)` at `src/auth.ts:45-92`

#### Line-by-Line Notes

- L45-48: Extracts `email` and `password` from `req.body`. **Assumption**: body is parsed JSON. **Verified**: Yes, middleware at `app.ts:12`.
- L50: Queries DB for user by email. **Assumption**: email is sanitized. **Verified**: No -- raw string interpolation. **FINDING: SQL injection risk**.
- L55-60: Compares password hash. Uses `bcrypt.compare()`. **OK**: timing-safe comparison.
- L62: Creates JWT token. **Assumption**: secret is strong. **Unverified**: need to check env config.

#### Invariants

- User must exist in DB before authentication succeeds
- Password comparison is timing-safe (bcrypt)
- JWT secret strength is unverified

#### Assumptions (Unverified)

- [ ] Email input is sanitized before DB query
- [ ] JWT secret is cryptographically random
- [ ] Session duration is bounded

#### Call Flow

authenticateUser() → findUserByEmail() → bcrypt.compare() → jwt.sign()

Phase 3: Cross-Function Flow Analysis

Goal: Trace data and control flow across function boundaries.

Steps

1. Select a critical data flow (e.g., user input to database query)
2. Trace forward: Follow the data from entry point through every transformation
3. At each boundary, document:
   • What validation occurs?
   • What transformation occurs?
   • Is the data type preserved or changed?
   • Are there implicit type coercions?
4. Build the flow diagram:

### Flow: User Login Input to Database

1. `req.body` (raw JSON) → Express body parser
2. `{ email, password }` (destructured) → `authenticateUser()`
3. `email` (string, UNVALIDATED) → `findUserByEmail(email)` ← RISK
4. `email` → SQL query template literal ← FINDING: injection
5. Result → `user` object (or null)
6. `password` + `user.passwordHash` → `bcrypt.compare()` ← OK

Phase 4: 5 Whys at Micro Scale

Apply 5 Whys to each finding or anomaly discovered:

### Finding: SQL injection in findUserByEmail

1. **Why** is there SQL injection? → Email is concatenated into query string
2. **Why** is it concatenated? → Developer used template literals instead of parameterized queries
3. **Why** no parameterized query? → The ORM wrapper doesn't enforce parameterization
4. **Why** no input validation? → No validation middleware for this route
5. **Why** no middleware? → Route was added without security review

Phase 5: 5 Hows at Micro Scale

Apply 5 Hows to verify implementation correctness:

### Verification: JWT Token Generation

1. **How** is the token created? → `jwt.sign(payload, secret, options)`
2. **How** is the secret managed? → `process.env.JWT_SECRET`
3. **How** is the secret rotated? → No rotation mechanism found
4. **How** is token expiry enforced? → `expiresIn: '24h'` in options
5. **How** is token revocation handled? → No revocation mechanism found

Output: Context Report

The final output is a structured context report:

# Audit Context Report: [Component Name]

## Summary

- Files analyzed: N
- Functions analyzed: N
- Findings: N (Critical: X, High: Y, Medium: Z)
- Unverified assumptions: N

## Mental Model

[High-level description of how the component works, backed by line references]

## Findings

[Each finding with line references, 5 Whys analysis, severity]

## Invariants

[All tracked invariants with verification status]

## Unverified Assumptions

[All assumptions that require further investigation]

## Call Flow Maps

[All traced data/control flows]

## Recommendations

[Prioritized list of actions based on findings]

Integration with Agent-Studio

Recommended Workflow

1. Invoke audit-context-building skill first for deep analysis
2. Feed findings into security-architect for threat modeling
3. Use variant-analysis skill to find similar patterns
4. Use static-analysis skill for automated confirmation

Complementary Skills

Skill	Relationship
security-architect	Consumes context reports for threat modeling
variant-analysis	Finds pattern variants across codebase
static-analysis	Automated confirmation of manual findings
differential-review	Reviews fixes for completeness
code-analyzer	Provides complexity metrics for prioritization

Anti-Patterns

Anti-Pattern	Why It Fails	Correct Approach
Skipping to conclusions from function names	Names describe intent, not behavior; leads to false findings	Read the code line-by-line before forming conclusions
Trusting comments without reading code	Comments are often wrong, stale, or misleading	Treat comments as hypotheses to verify against actual code
Skipping error paths in analysis	Security bugs often live in error handlers, not happy paths	Explicitly trace all error branches with equal rigor
Analyzing functions before mapping call flows	Misses cross-function trust assumptions and data flow	Map module/call graph in Phase 1 before deep analysis
Leaving assumptions untracked	Unverified assumptions silently become false findings	Mark every assumption [UNVERIFIED] until confirmed

Memory Protocol

Before starting: Read existing audit context from .claude/context/reports/backend/ for prior analysis of the same codebase area.

During analysis: Write incremental findings to context report file as you discover them. Do not wait until the end.

After completion: Record key findings and methodology notes to .claude/context/memory/learnings.md for future audit sessions.