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Comprehensive and Detailed Explanation:

Before defining a custom pattern for secret scanning in a repository, you must enable secret scanning for that repository. Secret scanning must be active to utilize custom patterns, which allow you to define specific formats (using regular expressions) for secrets unique to your organization.​

Once secret scanning is enabled, you can add custom patterns to detect and prevent the exposure of sensitive information tailored to your needs.​

To change the threshold that defines whether a pull request fails due to code scanning alerts (such as blocking merges based on severity), the user must have Admin access on the repository. This is because modifying these settings falls under repository configuration privileges.

Users with Write, Maintain, or Triage roles do not have the required access to modify rulesets or status check policies.

When you identify that a code scanning alert is a false positive—such as when your code uses a custom sanitization method not recognized by the analysis—you should dismiss the alert with the reason "false positive." This action helps improve the accuracy of future analyses and maintains the relevance of your security alerts.​

As per GitHub's documentation:​

"If you dismiss a CodeQL alert as a false positive result, for example because the code uses a sanitization library that isn't supported, consider contributing to the CodeQL repository and improving the analysis."​

By dismissing the alert appropriately, you ensure that your codebase's security alerts remain actionable and relevant.

A security policy is defined by a SECURITY.md file in the root of your repository or .github/ directory. This file informs contributors and security researchers about how to responsibly report vulnerabilities. It improves your project’s transparency and ensures timely communication and mitigation of any reported issues.

Adding this file also enables a “Report a vulnerability” button in the repository’s Security tab.

To proactively address secret scanning:

Webhooks can be configured to listen for secret scanning events. This allows automation, logging, or alerting in real-time when secrets are detected.

Documenting secure development practices (like using environment variables or secret managers) helps reduce the likelihood of developers committing secrets in the first place.

Dismissal based on age is not a best practice without triage. SCIM deals with user provisioning, not scanning alerts.

Comprehensive and Detailed Explanation:

Dependabot alerts are generated based on data from various sources:​

National Vulnerability Database (NVD): A comprehensive repository of known vulnerabilities, which GitHub integrates into its advisory database.​

GitHub Docs

Security Advisories Reported on GitHub: GitHub allows maintainers and security researchers to report and discuss vulnerabilities, which are then included in the advisory database.​

The dependency graph and manifest/lock files are tools used by GitHub to determine which dependencies are present in a repository but are not sources of vulnerability disclosures themselves.​

For compiled languages, CodeQL performs extraction by monitoring the normal build process. This means it watches your usual build commands (like make, javac, or dotnet build) and extracts the relevant data from the actual build steps being executed. CodeQL uses this information to construct a semantic database of the application.

This approach ensures that CodeQL captures a precise, real-world representation of the code and its behavior as it is compiled, including platform-specific configurations or conditional logic used during build.

Comprehensive and Detailed Explanation:

In private repositories, users with write access can fix code scanning alerts. They can do this by committing changes that address the issues identified by the code scanning tools. This level of access ensures that only trusted contributors can modify the code to resolve potential security vulnerabilities.​

GitHub Docs

Users with read or triage roles do not have the necessary permissions to make code changes, and the security manager role is primarily focused on managing security settings rather than directly modifying code.​

Secrets committed and then deleted are still accessible in the repository’s Git history. To locate them, navigate to the Commits tab. GitHub's secret scanning can detect secrets in both current and historical commits, which is why remediation should also include revoking the secret, not just removing it from the latest code.

A Dependabot alert is only marked as resolved when the related vulnerability is no longer present in your code — specifically after you merge a pull request that updates the vulnerable dependency.

Simply viewing alerts or graphs does not affect their status. Ignoring the alert by leaving the repo unchanged keeps the vulnerability active and unresolved.