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Gh Code Scanning

MicrosoftOfficialPublished by Microsoft

  • Skill
  • Tool integration
  • Software development
  • MIT
  • Low risk
  • Has scripts

From the author

Retrieves and groups GitHub code scanning alerts by rule and severity using the gh CLI
— the description by Microsoft

AutoGineer summary

Written by AutoGineer from the skill’s own files, not by the author

The gh-code-scanning skill provides a structured way to interact with GitHub code scanning alerts, which are otherwise difficult to access via standard toolsets. By utilizing the gh CLI, this skill allows users to fetch, group, and analyze security alerts from static analysis tools like CodeQL and Scorecard. It provides scripts for both PowerShell and Bash environments, ensuring that security data can be consumed programmatically in a consistent JSON format for triage and reporting.

What it does

  • Retrieves open code scanning alerts from GitHub repositories.
  • Groups alerts by rule ID and severity for easier analysis.
  • Supports filtering by branch and severity levels.
  • Identifies dismissed alerts that are still detected in the codebase.
  • Provides detailed JSON output including affected file paths and alert URLs.
  • Includes guidance on creating deduplicated security issues based on scan results.

When to use it

  • When you need to perform security triage on a GitHub repository.
  • When you need to programmatically aggregate code scanning findings.
  • When you want to identify which files are most affected by specific security rules.
  • When you need to track dismissed alerts that have not been fully resolved.

Advantages

  • Standardizes security alert data into a machine-readable JSON format.
  • Simplifies the triage process by grouping alerts by rule and severity.
  • Provides cross-platform support via PowerShell and Bash scripts.
  • Enables automated reporting and issue creation workflows.

Usage examples

“Get a summary of all open code scanning alerts for the repository microsoft/hve-core.”
The agent executes the PowerShell script to return a JSON array of grouped alerts, sorted by occurrence count, which the agent then presents to the user.
“List all critical severity code scanning alerts for the main branch of my-org/my-repo.”
The agent uses the bash script with the -s critical flag to filter and return the relevant alerts in JSON format.

Install

  1. Download the skill as a ZIP:

    https://autogineer.com/agent-skills/microsoft/gh-code-scanning/download
  2. Unzip it into the cross-client skills folder of your project:

    mkdir -p .agents/skills && unzip gh-code-scanning.zip -d .agents/skills

Documentation by Microsoft

GitHub Code Scanning Skill

Overview

GitHub code scanning alerts are produced by static analysis tools such as CodeQL and Scorecard and surfaced in the GitHub Security tab. The GitHub Security tab is not accessible through the default MCP toolset, so this skill provides scripts for all read operations.

Prerequisites

RequirementDetails
pwshPowerShell 7+; install from https://learn.microsoft.com/powershell
gh CLIInstalled and on PATH; install from https://cli.github.com
AuthRun gh auth login or set GH_TOKEN; requires security_events scope
Scopesecurity_events for private repos; public_repo for public-only

The repo scope also satisfies security_events. The gh CLI handles authentication automatically; no explicit token passing is needed in commands.

Get-CodeScanningAlerts.ps1 validates both prerequisites at startup and aborts with a targeted error message if either check fails.

Quick Start

Run this command to get a grouped summary of open code scanning alerts, sorted by frequency. This is the recommended first command when triaging a repository's code scanning posture.

pwsh scripts/Get-CodeScanningAlerts.ps1 -Owner "{owner}" -Repo "{repo}" -OutputFormat Json

This returns a JSON array of alert groups sorted by occurrence count, descending. Always use -OutputFormat Json when consuming results programmatically.

Parameters Reference

ParameterTypeRequiredDefaultDescription
-OwnerStringYesGitHub organization or user that owns the repository
-RepoStringYesRepository name
-OutputFormatStringNoTableOutput format: agents must always use Json for programmatic consumption; GroupedJson is accepted as an alias for Json
-BranchStringNomainBranch to scope alert results
-IncludeDismissedStillDetectedSwitchNoAlso report dismissed alerts that are still detected on the branch, as groups with Kind set to dismissed-still-detected

These parameters apply to Get-CodeScanningAlerts.ps1. For bash script flags including -s {severity} and -d, see the Script Reference section below.

Script Reference

Get-CodeScanningAlerts.ps1

Groups and sorts open code scanning alerts by occurrence count, descending.

# JSON output for programmatic consumption
pwsh scripts/Get-CodeScanningAlerts.ps1 -Owner "{owner}" -Repo "{repo}" -OutputFormat Json

# Scope to a specific branch
pwsh scripts/Get-CodeScanningAlerts.ps1 -Owner "{owner}" -Repo "{repo}" -Branch "{branch}" -OutputFormat Json

# Also report dismissed alerts that are still detected
pwsh scripts/Get-CodeScanningAlerts.ps1 -Owner "{owner}" -Repo "{repo}" -OutputFormat Json -IncludeDismissedStillDetected
get-code-scanning-alerts.sh

Groups and sorts open code scanning alerts by occurrence count, descending. Requires jq.

# JSON output for programmatic consumption
bash scripts/get-code-scanning-alerts.sh -o "{owner}" -r "{repo}"

# Scope to a specific branch
bash scripts/get-code-scanning-alerts.sh -o "{owner}" -r "{repo}" -b "{branch}"

# Filter by severity
bash scripts/get-code-scanning-alerts.sh -o "{owner}" -r "{repo}" -s critical

# Also report dismissed alerts that are still detected
bash scripts/get-code-scanning-alerts.sh -o "{owner}" -r "{repo}" -d

When to Use This Skill

Use this skill when the task involves reading code scanning alerts only. Get-CodeScanningAlerts.ps1 is the only supported method for listing and grouping code scanning alerts. gh api must not be used as a fallback for listing or grouping.

When the GitHub MCP server is configured with the code_security toolset, read-only access to code scanning alerts is available without gh api. Enable via toolsets: all or explicit toolset configuration.

Code Scanning Alerts

List and group open alerts

Always run with -OutputFormat Json. Parse the JSON output and present it to the user.

pwsh scripts/Get-CodeScanningAlerts.ps1 -Owner "{owner}" -Repo "{repo}" -OutputFormat Json

Use -Branch {branch} to scope to a branch other than main.

JSON output shape

-OutputFormat Json returns an array of group objects:

[
  {
    "RuleDescription": "Empty except",
    "RuleId": "py/empty-except",
    "Tool": "CodeQL",
    "SecuritySeverity": null,
    "Severity": "warning",
    "Count": 23,
    "AffectedPaths": [
      "scripts/plugins/Sync-PluginManifest.ps1",
      "scripts/linting/Validate-MarkdownFrontmatter.py"
    ],
    "HasFilePaths": true,
    "AlertUrl": "https://github.com/microsoft/hve-core/security/code-scanning/42",
    "FindingDescription": "'except' clause does nothing but pass and there is no explanatory comment."
  },
  {
    "RuleDescription": "Code injection",
    "RuleId": "actions/code-injection/medium",
    "Tool": "CodeQL",
    "SecuritySeverity": "medium",
    "Severity": "error",
    "Count": 2,
    "AffectedPaths": [
      ".github/workflows/validate.yml"
    ],
    "HasFilePaths": true,
    "AlertUrl": "https://github.com/microsoft/hve-core/security/code-scanning/17",
    "FindingDescription": "Potential code injection in ${{ inputs.version }}, which may be controlled by an external user."
  },
  {
    "RuleDescription": "Branch-Protection",
    "RuleId": "BranchProtectionID",
    "Tool": "Scorecard",
    "SecuritySeverity": "high",
    "Severity": "error",
    "Count": 1,
    "AffectedPaths": [],
    "HasFilePaths": false,
    "AlertUrl": "https://github.com/microsoft/hve-core/security/code-scanning/1",
    "FindingDescription": "score is 9: branch protection is not maximal on development and all release branches"
  }
]

SecuritySeverity is null for code quality rules that have no security classification; Severity (the non-security rule severity: error, warning, note, none) provides a fallback. AffectedPaths is always a JSON array of unique, sorted file paths with sentinel strings filtered out. HasFilePaths is false and AffectedPaths is [] when an alert has no associated source file (for example, BranchProtectionID). AlertUrl links directly to the alert in the GitHub Security tab. FindingDescription is the most recent alert message text.

With -IncludeDismissedStillDetected (or -d in bash), dismissed alerts whose most recent instance on the branch is not fixed are appended as separate groups after the open-alert groups. Those groups add Kind (dismissed-still-detected) and DismissedReason; open-alert groups are unchanged. A dismissal does not resolve an alert, so present these as alerts to reopen and fix.

Get single alert detail

This call returns one record; it is not a listing or grouping operation and does not conflict with the gh api restriction above.

gh api repos/{owner}/{repo}/code-scanning/alerts/{alert_number}
List affected file paths

Use -OutputFormat Json and read the AffectedPaths field from each rule group. The JSON output includes RuleDescription, RuleId, Tool, SecuritySeverity, Severity, Count, AffectedPaths (unique, sorted file paths), HasFilePaths (boolean: false for repo-level rules that have no associated source file), AlertUrl (string: direct link to the alert in the GitHub Security tab), and FindingDescription (string: most recent alert message text from the analysis tool) per group.

Key fields

These are GitHub API response field paths, not output object properties. The grouped output object field names are listed in the JSON output shape section above.

  • rule.security_severity_level: security severity tier: critical, high, medium, or low; null for code quality rules

  • rule.severity: non-security rule severity: error, warning, note, or none; always populated

  • rule.id: rule identifier used for deduplication and cross-referencing

  • tool.name: analysis tool that produced the alert (for example, CodeQL)

  • most_recent_instance.location.path: source file path of the most recent alert occurrence

Resolution policy

Resolve alerts in code or configuration. Never dismiss an alert, and never suggest dismissing one, including for false positives or test code. When a finding cannot be fixed yet, a maintainer can add a reviewed, expiring tracked exception; the alert stays open. Repositories that adopt this policy document it in their code-scanning alert lifecycle; for hve-core, see https://github.com/microsoft/hve-core/blob/main/docs/security/code-scanning-alert-lifecycle.md.

Code Scanning Analyses

These calls retrieve analysis metadata, not alert listings, and do not conflict with the gh api restriction above.

List recent analyses

Returns the last 10 CodeQL runs on the main branch.

gh api repos/{owner}/{repo}/code-scanning/analyses \
  -f tool_name=CodeQL \
  -f ref=refs/heads/main \
  -f per_page=10
Key fields
  • created_at: timestamp of the analysis run

  • results_count: number of alerts produced

  • rules_count: number of rules evaluated

  • tool.version: version of the analysis tool

  • warning / error: any issues reported during analysis

Backlog Issue Creation

Dedup check before creation

Search for an existing issue using the title and an embedded automation marker before creating a new one.

existing=$(gh issue list --repo "{owner}/{repo}" \
  --search "\"[Security] {rule_description}\" in:title" \
  --state open --json number --jq '.[0].number // empty')
if [[ -z "$existing" ]]; then
  gh issue create --repo "{owner}/{repo}" \
    --title "[Security] {rule_description}" \
    --label "security" \
    --body "<!-- automation:security-scan:{rule_id} -->
## Code Scanning Alert: {rule_description}

**Rule:** \`{rule_id}\`
$([ -n "{severity}" ] && echo "**Severity:** {severity}")
**Tool:** {tool}
**Affected files:** {count} occurrences

### Affected paths
{affected_paths}
"
fi

The automation marker <!-- automation:security-scan:{rule_id} --> is embedded in the issue body and serves as the deduplication anchor. Replace all {placeholders} with actual values from the alert-grouping JSON output.

Troubleshooting

SymptomLikely causeFix
gh CLI not found. Install it from https://cli.github.comgh CLI not on PATHInstall from https://cli.github.com, then re-open your terminal
gh CLI is not authenticated. Run 'gh auth login'gh auth not completedRun gh auth login; ensure security_events scope is granted
HTTP 403 Resource not accessible by integrationMissing security_events scope on tokenRe-authenticate: gh auth refresh -s security_events or set GH_TOKEN with appropriate scope
Empty results []Wrong ref format or no alerts on that branchOmit -f ref= to search all branches, or use refs/heads/main format (not just main)
bash: jq: command not foundjq not installedInstall via brew install jq (macOS), apt-get install jq (Debian/Ubuntu), or from https://jqlang.github.io/jq/

Files

scripts/Get-CodeScanningAlerts.ps1

#!/usr/bin/env pwsh
# Copyright (c) 2026 Microsoft Corporation. All rights reserved.
# SPDX-License-Identifier: MIT
#Requires -Version 7.4

<#
.SYNOPSIS
    Retrieves open code scanning alerts from a GitHub repository, grouped by rule.

.DESCRIPTION
    Uses the gh CLI to fetch open code scanning alerts for a repository and branch,
    suppressing the pager for non-interactive output. Results are grouped by rule
    description and sorted by occurrence count descending.

    Requires gh CLI authenticated with security_events scope (or public_repo for public repos).

.PARAMETER Owner
    GitHub organization or user name (e.g., 'microsoft').

.PARAMETER Repo
    Repository name without the owner (e.g., 'edge-ai').

.PARAMETER Branch
    Branch name to scope alerts to. Defaults to 'main'.

.PARAMETER OutputFormat
    Output format: Table (default), Json, or GroupedJson.
    - Table: Human-readable summary table.
    - Json: Full grouped alert objects as JSON array.
    - GroupedJson: Alias for Json; produces the same output.

.PARAMETER IncludeDismissedStillDetected
    Also report alerts that were dismissed but are still detected on the branch,
    meaning their most recent instance on the branch is not fixed. These groups
    are appended after the open-alert groups and carry
    Kind = 'dismissed-still-detected' and the DismissedReason of their first alert.
    Open-alert groups are unchanged. A dismissal never resolves an alert, so these
    alerts need to be reopened and resolved.

.EXAMPLE
    ./Get-CodeScanningAlerts.ps1 -Owner microsoft -Repo edge-ai

.EXAMPLE
    ./Get-CodeScanningAlerts.ps1 -Owner microsoft -Repo edge-ai -Branch develop -OutputFormat Json

.EXAMPLE
    ./Get-CodeScanningAlerts.ps1 -Owner microsoft -Repo edge-ai -OutputFormat Json -IncludeDismissedStillDetected
#>
[CmdletBinding()]
param(
    [Parameter(Mandatory = $true)]
    [ValidatePattern('^[a-zA-Z0-9._-]+$', ErrorMessage = 'Owner must contain only alphanumeric characters, dots, hyphens, or underscores.')]
    [string]$Owner,

    [Parameter(Mandatory = $true)]
    [ValidatePattern('^[a-zA-Z0-9._-]+$', ErrorMessage = 'Repo must contain only alphanumeric characters, dots, hyphens, or underscores.')]
    [string]$Repo,

    [Parameter()]
    [ValidatePattern('^[a-zA-Z0-9._/-]+$', ErrorMessage = 'Branch must contain only alphanumeric characters, dots, hyphens, underscores, or slashes.')]
    [string]$Branch = 'main',

    [Parameter()]
    [ValidateSet('Table', 'Json', 'GroupedJson')]
    [string]$OutputFormat = 'Table',

    [Parameter()]
    [switch]$IncludeDismissedStillDetected
)

$ErrorActionPreference = 'Stop'

function Get-AlertPage {
    param([Parameter(Mandatory = $true)][string]$Url)

    $raw = gh api $Url --paginate --jq '.[]'

    if ($LASTEXITCODE -ne 0) {
        if ($raw -match '403|Resource not accessible by integration') {
            Write-Error "gh api call failed: missing required scope. Run 'gh auth refresh -s security_events' and re-run this script."
        }
        Write-Error "gh api call failed (exit $LASTEXITCODE): $raw"
    }

    return , @($raw | ConvertFrom-Json)
}

function ConvertTo-AlertGroup {
    param([Parameter(Mandatory = $true)][AllowEmptyCollection()][object[]]$Alerts)

    $Alerts |
        Group-Object { $_.rule.description } |
        ForEach-Object {
            $paths = @(
                $_.Group |
                ForEach-Object { $_.most_recent_instance.location.path } |
                Where-Object { $_ -and $_ -ne 'no file associated with this alert' } |
                Sort-Object -Unique
            )
            [PSCustomObject]@{
                RuleDescription    = $_.Name
                RuleId             = $_.Group[0].rule.id
                Tool               = $_.Group[0].tool.name
                SecuritySeverity   = $_.Group[0].rule.security_severity_level
                Severity           = $_.Group[0].rule.severity
                Count              = $_.Count
                AffectedPaths      = $paths
                HasFilePaths       = ($paths.Count -gt 0)
                AlertUrl           = $_.Group[0].html_url
                FindingDescription = $_.Group[0].most_recent_instance.message.text
            }
        } |
        Sort-Object -Property Count -Descending
}

#region Main Execution

if ($MyInvocation.InvocationName -ne '.') {
    $env:GH_PAGER = ''

    if (-not (Get-Command gh -ErrorAction SilentlyContinue)) {
        Write-Error "gh CLI not found. Install it from https://cli.github.com and re-run this script."
    }

    gh auth status 2>&1 | Out-Null
    if ($LASTEXITCODE -ne 0) {
        Write-Error "gh CLI is not authenticated. Run 'gh auth login' and ensure the 'security_events' scope is granted, then re-run this script."
    }

    $Url = "repos/$Owner/$Repo/code-scanning/alerts?state=open&ref=refs/heads/$Branch&per_page=100"
    $Alerts = Get-AlertPage -Url $Url
    $Grouped = @(ConvertTo-AlertGroup -Alerts $Alerts)

    if ($IncludeDismissedStillDetected) {
        # The ref filter scopes most_recent_instance to the branch. A dismissed alert
        # whose instance there is not 'fixed' is still being detected.
        $DismissedUrl = "repos/$Owner/$Repo/code-scanning/alerts?state=dismissed&ref=refs/heads/$Branch&per_page=100"
        $Dismissed = Get-AlertPage -Url $DismissedUrl
        $StillDetected = @($Dismissed | Where-Object { $_.most_recent_instance.state -ne 'fixed' })
        foreach ($group in @(ConvertTo-AlertGroup -Alerts $StillDetected)) {
            $first = $StillDetected | Where-Object { $_.rule.id -eq $group.RuleId } | Select-Object -First 1
            $group | Add-Member -NotePropertyName Kind -NotePropertyValue 'dismissed-still-detected'
            $group | Add-Member -NotePropertyName DismissedReason -NotePropertyValue $first.dismissed_reason
            $Grouped += $group
        }
    }

    switch ($OutputFormat) {
        'Table' {
            $columns = @('Count', 'SecuritySeverity', 'RuleId', 'RuleDescription')
            if ($IncludeDismissedStillDetected) { $columns += 'Kind' }
            $Grouped | Format-Table -AutoSize -Property $columns
        }
        { $_ -in 'Json', 'GroupedJson' } {
            # The array wrapper keeps the output a JSON array for every result size.
            # Piping to ConvertTo-Json emits a bare object for a single group and nothing at all for none.
            ConvertTo-Json -InputObject @($Grouped) -Depth 5
        }
    }

    exit 0
}

#endregion Main Execution

Requirements and compatibility

Written for: GitHub Copilot

Works with: Claude Code, Claude apps, OpenAI Codex, GitHub Copilot, Cursor, Gemini CLI, Kiro, OpenCode, Goose, Amp, Roo Code, JetBrains Junie, Factory Droid, Devin (ex-Windsurf), Mistral Vibe, OpenHands, Letta

“Works with” means the tool reads the open Agent Skills format; a skill written for one tool may use features others lack.

Needs: Needs an MCP server, Needs a command-line tool

The author says: Requires pwsh 7+ and gh CLI authenticated with the security_events scope. Bash script requires jq.

Security

What our scanner noticed· Low risk

  • Scripts that your agent may run

This skill includes scripts that your agent may run. Read them before you use it.

A static scan is not a guarantee. Skills are third-party content: review a skill before you let an agent use it.

Attribution and licence

Published by
Microsoft
Publisher
Microsoft (Official)
Source
microsoft/hve-core · .github/skills/security/gh-code-scanning · commit f425e94
Licence
MIT License (redistribution allowed)
  • LICENSE (added by AutoGineer from LICENSE)
  • ATTRIBUTION.md (written by AutoGineer)
Synced

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Download ZIP

The ZIP holds the skill’s files, its licence files and an ATTRIBUTION.md. Download gh-code-scanning.zip