Run

AppSec Run -- Smart Orchestrator

The primary way to run security analysis. Detects the project's tech stack, selects the most relevant scanners and category skills, runs everything in parallel, consolidates results, and optionally launches red team simulation.

This skill is the automated version of /appsec:start. Where start gives recommendations and lets the user choose, run makes the choices and executes them. It handles ALL cross-cutting flags and adapts its behavior to the detected codebase.

Supported Flags

Read ../../shared/schemas/flags.md for the full flag specification. This orchestrator supports ALL cross-cutting flags.

Workflow

Phase 1: Detection (Main Agent)

Execute these steps sequentially in the main agent context before launching any subagents. Use Glob, Grep, Read, and Bash tools to gather evidence.

Step 1.1: Check for Cached Assessment

Look for .appsec/start-assessment.json. If it exists and is fresh (less than 24 hours old, and manifest files have not changed since), load it and skip to Step 1.5.

The cached assessment is also stale if any of:

• Scanner availability has changed (a new scanner was installed or one was removed)
• .appsec/config.yaml has been modified since the assessment
• The current git branch differs from the branch recorded in the assessment

If no cache exists or it is stale, run Steps 1.2 through 1.4.

Step 1.2: Detect Tech Stack

Read project manifests to determine languages, frameworks, and databases. Check for each of these files using Glob:

Read each found manifest to extract framework names and notable dependencies.

Step 1.3: Detect Architecture & Data Sensitivity

Scan for patterns indicating sensitive data and architecture type:

Architecture signals:

• API-only: route handlers without templates, OpenAPI spec
• Full-stack: template engines alongside API, React/Vue/Angular
• GraphQL: .graphql files, graphql in dependencies
• WebSocket: ws, socket.io in dependencies
• Serverless: Lambda handlers, Cloud Functions

Data sensitivity signals:

• PII: email, phone, ssn, date_of_birth in models
• Financial: stripe, paypal, card_number, transaction
• Health: hipaa, patient, diagnosis, medical_record
• Auth: jwt, oauth, bcrypt, session

Step 1.4: Detect Installed Scanners

Check PATH for known scanner binaries using Bash which commands. Run these checks in parallel:

which semgrep && which bandit && which gosec && which brakeman
which gitleaks && which trufflehog && which trivy && which osv-scanner
which npm && which pip-audit && which cargo-audit

Read ../../shared/schemas/scanners.md for the full scanner registry. Only mark language-specific scanners as relevant if that language is in the detected stack.

Step 1.5: Build Execution Plan

Based on detected stack, data sensitivity, architecture, and installed scanners, build an execution plan that determines:

1. Which scanners to run (only those installed and relevant).
2. Which category skills to dispatch (based on architecture and data).
3. Which frameworks to use (OWASP is always included; STRIDE added for apps with user auth; LINDDUN added when PII detected).

Tool selection rules:

If --only is specified, override the automatic selection and dispatch only the listed tools/categories.

Cache the execution plan to .appsec/start-assessment.json with a timestamp for future reuse.

Phase 2: Run Scanners (Main Agent)

Run detected scanners in the main agent context using Bash. Launch ALL scanner commands in parallel Bash calls within a SINGLE response.

Before launching scanners, create the output directory:

mkdir -p reports/appsec/scanners

For each detected scanner, use the invocation pattern from ../../shared/schemas/scanners.md. Redirect ALL scanner output to files — the main agent NEVER reads scanner JSON content.

Scanner dispatch pattern:

# Run each scanner in parallel Bash calls — redirect output to files
semgrep scan --config auto --json --quiet <scope_path> > reports/appsec/scanners/semgrep.json 2>&1
gitleaks detect --source <scope_path> --report-format json --no-banner > reports/appsec/scanners/gitleaks.json 2>&1
npm audit --json > reports/appsec/scanners/npm-audit.json 2>&1           # if Node.js project
pip-audit --format json > reports/appsec/scanners/pip-audit.json 2>&1    # if Python project
trivy fs --format json <scope_path> > reports/appsec/scanners/trivy.json 2>&1   # if installed

After ALL scanners complete, check exit codes and file sizes ONLY. Do NOT read or parse scanner JSON files in the main agent context.

# Check each scanner result — exit code + file size only
ls -l reports/appsec/scanners/*.json

Build a scanner status list from exit codes and file sizes:

• Exit code 0 or 1 AND file size > 0: Mark as OK.
• Exit code > 1 AND file size > 0: Mark as PARTIAL (ran with warnings).
• File size 0 or file missing: Mark as FAILED (no output).
• Exit code 127 (command not found): Mark as MISSING.

Error handling for scanners:

• Non-zero exit code: Many scanners exit non-zero when they find issues (e.g., npm audit exits 1 when vulnerabilities exist). This is normal. Only treat it as a failure if the output file is empty (0 bytes).
• Timeout: If a scanner does not return within 120 seconds, skip it and note the timeout. Mark as FAILED (timeout).
• Scanner not found: If a scanner from the plan is not installed (exit code 127), note it in SCANNERS MISSING and continue.
• Track all scanner statuses for the consolidator:

  scanner_status = []  # list of {scanner, status, file_path, file_size}
  

If --depth quick is set, skip Phases 3 and 4. Jump directly to Phase 5 and launch the consolidator subagent with scanner results only.

Phase 3: Dispatch Category Skills (Parallel Subagents)

CRITICAL: All Task tool calls MUST appear in the SAME response message. This is what triggers parallel execution. If you emit them across separate messages, they run sequentially and waste time.

For each tool in the execution plan, launch a subagent Task call.

Resolving the Scope

Before dispatching, resolve the scope to a concrete file list:

Empty scope handling: If the resolved file list is empty (e.g., --scope changed on a clean working tree, or --scope staged with nothing staged), do NOT silently proceed with an empty analysis. Instead:

1. Inform the user that the scope resolved to zero files.
2. Suggest alternatives: --scope full for the entire repo, --scope branch for all branch changes, or stage some changes first.
3. Do NOT dispatch any subagents or scanners. Exit early.

For specific scope types, provide actionable error messages:

• --scope file:<path>: If the file does not exist, report "File not found: <path>" and suggest similar filenames using Glob.
• --scope path:<dir>: If the directory does not exist, report "Directory not found: <dir>".
• --scope module:<name>: If the module cannot be located, report "Module not found: <name>".
• --scope branch: If on the base branch with no divergence, report "No commits ahead of base branch."

Subagent Prompt Template

Before dispatching, create the output directory:

mkdir -p reports/appsec/skills

Each subagent Task call must include a FULLY self-contained prompt. Subagents get their own isolated context window and cannot see the main conversation. Subagents write their findings to a file and return ONLY a one-line status summary.

Analyze the following files for {TOOL_DESCRIPTION} vulnerabilities:

FILES:
{FILE_LIST}

STEP 1: Read the skill definition at:
{ABSOLUTE_PATH_TO_PLUGIN}/skills/{SKILL_NAME}/SKILL.md

STEP 2: Follow the workflow defined in that skill to analyze the listed files.

STEP 3: Read the findings schema at:
{ABSOLUTE_PATH_TO_PLUGIN}/shared/schemas/findings.md

STEP 4: Produce findings in the schema format. Set metadata.tool to "{TOOL_NAME}"
and metadata.framework to "{FRAMEWORK}".

STEP 5: Write findings using the AGGREGATE OUTPUT format from the findings schema to:
{ABSOLUTE_PATH_TO_PROJECT}/reports/appsec/skills/{TOOL_NAME}.json

Use the Write tool. The file must be a JSON object with fields:
  tool, total_findings, by_severity (object with critical/high/medium/low counts),
  notes (optional string), findings (array)

The notes field is optional. If the skill produces narrative assessment beyond
structured findings, include it here.

If zero findings, write: {"tool":"{TOOL_NAME}","total_findings":0,"by_severity":{"critical":0,"high":0,"medium":0,"low":0},"findings":[]}

FLAGS: --scope {SCOPE} --depth {DEPTH} --severity {SEVERITY}

IMPORTANT: After writing the file, return ONLY a one-line status in this exact format:
"{TOOL_NAME}: N findings (Xc Xh Xm Xl)"
where N is the total count and Xc/Xh/Xm/Xl are counts per severity.
Do NOT return the findings themselves. Do NOT produce a summary or
cross-tool analysis. The orchestrator handles consolidation.

Launching

Emit ALL Task tool calls in a single response:

• subagent_type: "general-purpose"
• description: "{TOOL_NAME} - {SHORT_DESCRIPTION}"
• prompt: The fully self-contained prompt above, filled in for this tool.

Do NOT emit Task calls one at a time. Do NOT wait between dispatches.

Phase 4: Red Team Simulation (Expert Mode Only)

If --depth expert is set and --skip-redteam is NOT set, launch red team agents AFTER Phase 3 subagents complete. Red team agents read prior findings from files to build multi-step attack chains.

Before dispatching, create the output directory:

mkdir -p reports/appsec/redteam

Red Team Agent Registry

By default, launch all 6 agents. If --persona is specified, launch only the listed personas.

CRITICAL: All 6 (or selected) red team Task calls MUST appear in the SAME response message for parallel execution.

Red Team Subagent Prompt Template

You are a red team agent. Read your persona definition at:
{ABSOLUTE_PATH_TO_PLUGIN}/agents/{PERSONA_NAME}.md

Analyze the following codebase for exploitable vulnerabilities from your persona's
perspective:

FILES:
{FILE_LIST}

STEP 1: Read prior findings from these directories using the Read tool:
- {ABSOLUTE_PATH_TO_PROJECT}/reports/appsec/scanners/*.json
- {ABSOLUTE_PATH_TO_PROJECT}/reports/appsec/skills/*.json
These contain the automated analysis results. Use Glob to list the files, then
read each one.

STEP 2: Read the findings schema at:
{ABSOLUTE_PATH_TO_PLUGIN}/shared/schemas/findings.md

STEP 3: Read the DREAD scoring framework at:
{ABSOLUTE_PATH_TO_PLUGIN}/shared/frameworks/dread.md

STEP 4: Attempt to chain vulnerabilities into multi-step attack scenarios.
Score each finding using DREAD.

STEP 5: Write findings using the AGGREGATE OUTPUT format from the findings schema to:
{ABSOLUTE_PATH_TO_PROJECT}/reports/appsec/redteam/{PERSONA_NAME}.json

Use the Write tool. The file must be a JSON object with fields:
  tool, total_findings, by_severity (object with critical/high/medium/low counts), findings (array)

If zero findings, write: {"tool":"{PERSONA_NAME}","total_findings":0,"by_severity":{"critical":0,"high":0,"medium":0,"low":0},"findings":[]}

Use "RT" prefix for finding IDs.

IMPORTANT: After writing the file, return ONLY a one-line status in this exact format:
"{PERSONA_NAME}: N findings (Xc Xh Xm Xl)"
where N is the total count and Xc/Xh/Xm/Xl are counts per severity (critical, high, medium, low).
Example: "insider: 4 findings (1c 2h 1m 0l)"
Do NOT return the findings themselves.

Phase 5: Consolidation (Consolidator Subagent)

After ALL subagents (category skills and optionally red team agents) return, the main agent builds a status summary and launches ONE consolidator subagent.

Build Status Summary

From each subagent's one-line status return, build two lists:

tools_ok = []      # e.g. ["injection: 3 findings (0c 1h 2m 0l)", ...]
tools_failed = []  # e.g. ["crypto: empty output", "ssrf: error ..."]

A subagent result goes into tools_failed if:

• The Task tool returned an error or exception message
• The subagent returned an empty string
• The subagent's output does not match the pattern "{TOOL_NAME}: N findings (...)"

Record the tool name and the first 100 characters of the response as the error reason.

Do NOT re-read any findings files in the main agent context.

Also include scanner statuses from Phase 2:

scanners_ok = []      # e.g. ["semgrep: OK", "npm-audit: OK"]
scanners_failed = []  # e.g. ["gitleaks: FAILED (timeout)"]
scanners_missing = [] # e.g. ["trivy", "bandit"]

Launch Consolidator Subagent

Launch a single consolidator subagent with the following FULLY self-contained prompt. This subagent reads all result files, merges, deduplicates, and produces the final report.

You are the appsec consolidator. Your job is to merge all security findings
from scanners, category skills, and red team agents into a single deduplicated
report.

STEP 1: Read the findings schema at:
{ABSOLUTE_PATH_TO_PLUGIN}/shared/schemas/findings.md

STEP 2: Read all JSON result files from these directories using Glob + Read:
- {ABSOLUTE_PATH_TO_PROJECT}/reports/appsec/scanners/*.json
- {ABSOLUTE_PATH_TO_PROJECT}/reports/appsec/skills/*.json
- {ABSOLUTE_PATH_TO_PROJECT}/reports/appsec/redteam/*.json  (if directory exists)

For scanner files: each scanner produces its own JSON format. Read the scanner
registry and format reference at:
{ABSOLUTE_PATH_TO_PLUGIN}/shared/schemas/scanners.md

Convert scanner findings to the standard schema format. Set scanner.confirmed
to true and scanner.name to the scanner name (derived from the filename,
e.g. "semgrep.json" -> "semgrep").

For skill and red team files: these already use the standard schema format.

If any file contains malformed JSON that cannot be parsed, log the filename
in a TOOLS DEGRADED list and skip it. Continue processing other files.

STEP 3: Deduplicate findings.
Two findings are duplicates if they share the same location.file AND
location.line (or overlapping line ranges). When duplicates exist:
- Keep the finding with the higher severity.
- Merge cross-framework references from both.
- Prefer scanner-confirmed findings over heuristic-only.
- Note the duplicate source in the retained finding's description.

STEP 4: Cross-reference each finding. Populate:
- references.cwe: CWE identifier
- references.owasp: OWASP Top 10 category
- references.stride: STRIDE category letter(s)
- references.mitre_attck: ATT&CK technique ID
- references.sans_cwe25: SANS/CWE Top 25 rank if applicable

STEP 5: Rank findings.
Sort: critical > high > medium > low. Within the same severity, sort by
confidence (high > medium > low). Within the same confidence,
scanner-confirmed findings rank higher.

STEP 6: Apply severity filter.
If SEVERITY_FILTER is set to a value other than "low" or empty, remove all
findings with severity below that threshold. Severity ranking from highest to
lowest: critical > high > medium > low. If no filter, include all findings.

STEP 7: Write consolidated output files using the Write tool.

First ensure the output directory exists:
  mkdir -p {ABSOLUTE_PATH_TO_PROJECT}/.appsec

Then write:
- {ABSOLUTE_PATH_TO_PROJECT}/.appsec/findings.json — the full findings array
  in the aggregate schema format (for downstream skills like /appsec:status,
  /appsec:fix)
- {ABSOLUTE_PATH_TO_PROJECT}/.appsec/last-run.json — run metadata:
  {{"timestamp": "<ISO 8601>", "scope": "{SCOPE}", "depth": "{DEPTH}",
    "tools_run": [...], "tools_failed": [...], "scanners_used": [...],
    "scanners_missing": [...], "total_findings": N,
    "by_severity": {{"critical": N, "high": N, "medium": N, "low": N}}}}

STEP 8: Return the formatted report in {FORMAT} format.

TOOL STATUS (from orchestrator):
Tools OK: {TOOLS_OK_LIST}
Tools failed: {TOOLS_FAILED_LIST}
Scanners OK: {SCANNERS_OK_LIST}
Scanners failed: {SCANNERS_FAILED_LIST}
Scanners missing: {SCANNERS_MISSING_LIST}

CONTEXT:
Scope: {SCOPE}
Depth: {DEPTH}
Stack: {DETECTED_STACK}

For TEXT format (default), use this exact template:

=====================================================
              APPSEC RUN -- Security Scan
=====================================================

SCOPE: {SCOPE_DESCRIPTION}
DEPTH: {DEPTH}
STACK: {DETECTED_STACK}
SCANNERS: <scanner1> OK (N findings)  <scanner2> PARTIAL (warnings)  <scanner3> N/A
WARNINGS:                   (only if any category fell back to pattern-based analysis)
  <category>: No scanner installed. Detection is pattern-based only (higher false-negative risk).
  Recommended: Install <scanner-names> for reliable detection.

FINDINGS: <total> (<critical> critical, <high> high, <medium> medium, <low> low)

---  CRITICAL  ---

  [CRIT-1] <ID>: <title>
  File: <path>:<line>
  <description>
  Fix: <fix.summary>

  [CRIT-2] ...

---  HIGH  ---

  [HIGH-1] ...

---  MEDIUM  ---

  ...

---  LOW  ---

  ...

TOOLS RUN: <list of tools/categories from Tools OK>
TOOLS FAILED: <list from Tools failed, with reasons>
TOOLS DEGRADED: <list of files with malformed JSON, if any>
SCANNERS MISSING: <list from Scanners missing>

=====================================================
  <total> findings saved to .appsec/findings.json
  Run /appsec:explain <ID> for details on any finding
  Run /appsec:run --fix to auto-generate fixes
=====================================================

For JSON format: output the aggregate format from the findings schema.
For SARIF format: output SARIF 2.1.0 for GitHub Security tab integration.
For MARKDOWN format: output a Markdown report with headings, tables, and
code blocks.

IMPORTANT: Return ONLY the formatted report. The orchestrator will present
it directly to the user.

Phase 6: Output

Present the consolidator subagent's returned output directly to the user. The consolidator already produces the final formatted report (text, JSON, SARIF, or Markdown), so no reformatting is needed in the main agent.

Caching and State

After each run, state is written to .appsec/:

Intermediate results persist in reports/appsec/ (subdirectories: scanners/, skills/, redteam/) until the next run overwrites them.

This state powers /appsec:status and enables delta detection on subsequent runs.

Follow-Up Prompt

After presenting results:

Next steps:
  /appsec:explain <ID>         Explain any finding in detail
  /appsec:run --fix            Re-run and auto-generate fixes
  /appsec:run --depth expert   Add red team simulation
  /appsec:full-audit           Exhaustive audit with dated report
  /appsec:status               View security dashboard