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Security audit

Phy Large Codebase Workflow

Security checks for vulnerabilities and agentic risk

Overview

This is a documentation-only Claude Code workflow guide, with some powerful but disclosed examples users should run deliberately.

Install only if you intentionally want Claude Code large-repository workflow advice. Treat the batch-edit, commit, PR, CI, and resume examples as actions requiring deliberate approval, especially for private repositories or code that should not be sent to an external Claude account.

A.I.G

Vulnerability Patterns
  • Skill Instruction HijackingAlters the agent's session goals or safety constraints when the skill loads
  • Agent Memory PoisoningWrites attacker-controlled rules into memory that affect later sessions
  • Remote Payload Retrieval and ExecutionFetches external code whose behavior can change after review
  • Embedded Malicious CodeShips malicious scripts inside the skill and executes them locally
  • Unauthorized Access and Privilege EscalationObtains permissions beyond the task's legitimate needs

SkillSpector

Vulnerability Patterns
  • Excessive AgencyUnrestricted Tool Access, Autonomous Decision Making, Scope Creep
  • Rogue AgentSelf-Modification, Session Persistence
  • Prompt InjectionInstruction Override, Hidden Instructions, Exfiltration Commands
  • Data ExfiltrationExternal Transmission, Env Variable Harvesting, File System Enumeration
  • Privilege EscalationExcessive Permissions, Sudo/Root Execution, Credential Access
Findings (8)

External Model or Provider Selection

High
Category
Excessive Agency
Confidence
90% confidence
Finding

Skill selects an external model or provider that may use a different account or billing plan than the operator expects. Undisclosed model switches can cause unexpected cost or quota consumption.

Content

Scanner excerpt · SKILL.md (reported line 85)May include surrounding context.

Auto-Generate Codemap (One-Time)

bash
claude -p "Analyze this codebase and create a comprehensive codemap.
Output to .claude/codemaps/architecture.md. Include:
- Entry points
- Module responsibilities

External Model or Provider Selection

High
Category
Excessive Agency
Confidence
90% confidence
Finding

Skill selects an external model or provider that may use a different account or billing plan than the operator expects. Undisclosed model switches can cause unexpected cost or quota consumption.

Content

Scanner excerpt · SKILL.md (reported line 118)May include surrounding context.

bash
# After major refactors, regenerate
claude -p "Update .claude/codemaps/architecture.md based on current codebase structure"

External Model or Provider Selection

High
Category
Excessive Agency
Confidence
90% confidence
Finding

Skill selects an external model or provider that may use a different account or billing plan than the operator expects. Undisclosed model switches can cause unexpected cost or quota consumption.

Content

Scanner excerpt · SKILL.md (reported line 224)May include surrounding context.

bash
# Batch migrate files
for file in $(cat files.txt); do
  claude -p "Migrate $file from React to Vue. Return OK or FAIL." \
    --allowedTools "Edit,Bash(git commit:*)"
done

External Model or Provider Selection

High
Category
Excessive Agency
Confidence
90% confidence
Finding

Skill selects an external model or provider that may use a different account or billing plan than the operator expects. Undisclosed model switches can cause unexpected cost or quota consumption.

Content

Scanner excerpt · SKILL.md (reported line 229)May include surrounding context.

done

CI integration

claude -p "Analyze this PR for security issues" --output-format json

text

---

External Model or Provider Selection

High
Category
Excessive Agency
Confidence
90% confidence
Finding

Skill selects an external model or provider that may use a different account or billing plan than the operator expects. Undisclosed model switches can cause unexpected cost or quota consumption.

Content

Scanner excerpt · SKILL.md (reported line 277)May include surrounding context.

git worktree + multiple claude sessions

Generate/update codemap

claude -p "Create codemap for this project → .claude/codemaps/"

text

## Context Budget Rule of Thumb

Missing User Warnings

Medium
Category
Not specified by scanner
Confidence
95% confidence
Finding

The skill explicitly instructs the agent to 'commit with descriptive message and open a PR' without requiring an explicit user confirmation step or warning that this will modify repository state and potentially publish changes remotely. In an automation-oriented workflow skill, normalizing autonomous commits/PRs increases the chance of unintended code publication or persistence of unsafe changes.

Content

No source excerpt is available for this finding.

Missing User Warnings

Medium
Category
Not specified by scanner
Confidence
97% confidence
Finding

The batch automation example permits Edit plus Bash access scoped to 'git commit:*' inside a loop, enabling repeated repository-modifying actions across many files with no confirmation or review checkpoint. In batch mode, mistakes scale quickly and can create many unwanted commits or mass changes that are hard to audit or revert.

Content

No source excerpt is available for this finding.

Session Persistence

Medium
Category
Rogue Agent
Confidence
55% confidence
Finding

Skill establishes unauthorized persistence across sessions via cron jobs, startup scripts, or state files. Session persistence allows an attacker to maintain access beyond the current interaction.

Content

Scanner excerpt · SKILL.md (reported line 264)May include surrounding context.

md
/compact "Focus on API changes"  # At 70%
/clear                           # Between tasks

# Resume previous session (preserve context)
claude --continue                # Resume last session
claude --resume                  # Pick from history