Code Repository Settings
The Code Repository Settings screen lets you manage how Checkmarx One integrates with your connected code repositories — controlling which organizations and repos are synced, what permissions are granted, and which scan types run automatically when code changes.
This screen has two tabs, Organizations (default) and Custom Integrations.
Organizations (default) - configure integration settings for SCM (Source Control Management) organizations connected to Checkmarx One, at the organization level.
Custom Integrations - manage custom code repository integration instances.
Each tab label displays a live count of connected items (e.g., Organizations (157), Custom Integrations (80)), so you can see integration volume at a glance.
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Organizations
The Organizations tab lists all SCM organizations connected to Checkmarx One, including those set up via both managed and custom integration flows. You can filter this list by SCM type: GitHub, GitHub App, GitLab, Azure, and Bitbucket.
Each organization in the list shows a summary of its current sync status, permissions, and scan type settings, so you can see its configuration at a glance without opening the settings panel.
Managing the organization list
Click Refresh Organization Data to update the list of connected organizations. This action also cleans up the list: any imported organization that has no active Checkmarx One project and doesn't have Monitor New Repositories enabled will be removed from the integration.
To configure an organization, click it to open its settings panel.
Organization Settings Panel
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When you click into an organization, its settings panel opens, divided into three sections: Auto Sync, Permissions, and Scan Type. After making changes in any section, click Save to apply them.
Each setting in the Permissions and Scan Type sections can also be locked or left open for override at the project level — see Allow or Block Override below.
Auto Sync
Notice
Available for GitHub, GitHub Apps, and Azure DevOps.
Auto Sync provides the Monitor New Repositories functionality for an organization. It contains a single toggle: Automatically sync new projects created for this organization.
When enabled, Checkmarx monitors your SCM for new repositories. Any new repo is automatically onboarded as a Code Repository Integration project within that organization in Checkmarx One, inheriting its settings from the organization-level configuration.
Permissions
Toggle the permissions you want to adjust, then click Save. If you activate a new permission, you must also click Refresh Organization Permissions (see below) before it takes effect.
Pull Request Decoration - Automatically sends the scan results summary to the SCM. (Default: On)
AI Triage & Remediation - Enables AI Triage and AI Remediation for the projects associated with this organization. During pull request scans, eligible new vulnerabilities are automatically analyzed, and developers can request AI-generated fixes directly from the pull request. When enabled, an Applies to severities dropdown becomes available, letting you scope AI Triage & Remediation to only the vulnerability severities you select (e.g., Critical and High).
Refreshing organization permissions
Click the 
icon to refresh organization permissions. A pop-up opens where you choose an authentication method, then click Refresh Permission to apply.
Scan Type
Toggle the scanners that will run for this organization's automatic scans, then click Save. Options are SAST, SCA, IaC Security, Container Security, API Security, OSSF Scorecard, Secret Detection.
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In addition, in this section you can configure the following:
SAST Incremental Scan - Configure SAST scans to run as Incremental scans. (Default: Off) For additional info, see Incremental Scans.
SCA Auto Pull Request - Automatically send PRs to your SCM with recommended changes in the manifest file, in order to replace the vulnerable package versions. (Default: Off)
Allow or Block Override
When a new organization is created, the settings configured at that time are applied to the organization entity in Checkmarx. By default, every setting allows override at the project level.
In the Permissions and Scan Type sections, each setting has an Allow Override checkbox. Deselecting it prevents that setting from being overridden at the project level.
How editing organization settings affects child projects:
Existing Projects | New Projects (Auto Sync) | New Projects (New Project flow / Migration) | |
|---|---|---|---|
Allow Override enabled | Keep their original configuration | Inherit the edited organization settings | Organization settings shown by default, but adjustable by the user |
Allow Override disabled | Inherit the edited organization settings | Inherit the edited organization settings | Inherit organization settings; controls are greyed out and can't be adjusted |
Notice
If Allow Override is disabled for a setting and later re-enabled, existing projects revert to their original setting (the one they had before the edit).
Notice
Preventing overrides only applies to automatically triggered scans (e.g., pull request scans). If you manually trigger a scan of a project — via UI, CLI, or API — you have complete autonomy to override these settings for that particular scan.
Custom Integrations
This tab lists the custom code repository integrations in your Checkmarx One account. You can edit the configuration of custom code repository instances or delete existing ones.
The list also shows an Associated Projects column with a live project count for each configuration — useful for checking whether a configuration can be deleted (see Deleting a custom configuration below) before you even open it.
These settings apply only to the code repository integration itself. Scan settings for organizations associated with the integration are configured separately, in the Organizations tab under the relevant organization's settings.
Note
Only users with update-tenant-params permission can edit and delete repo configurations.
Editing a custom configuration:
Hover over the actions menu
at the end of the row for the configurationyou want to edit and select Edit.A side panel opens showing the current configuration.
Adjust the values as needed.
Click Save.
The new configuration is applied.
Notice
If there are existing Checkmarx One Projects associated with this configuration, a warning note explains that changing the configuration will affect those Projects. Click on the View projects link to view the list of associated Projects.
Deleting a custom configuration:
Warning
You can only delete a configuration if no projects are associated with it. If there are associated projects, you need to first delete the projects and then delete the configuration. You can access the list of associated projects by hovering on the info icon and then clicking on show projects.
Hover over the actions menu
at the end of the row of the desired configuration and select Delete.In the confirmation dialog, click Delete Configuration.