After using the Commit Changes feature in the Source Control menu in Studio, the commit completes successfully, but some of the changed files are still appearing in the list and the Commit Changes option is still available.
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When an application is committed to source control, the system searches for sys_update_xml records in order to determine what local changes are being committed. When the commit is finished, the system deletes these sys_update_xml records. However, the system will only remove them if they are inside a valid update set that is part of the application.
If files are still appearing in this list after committing, it indicates an issue with the update set they are in. Find these updates by going to the sys_update_xml table and searching for records where the Application field is equal to the affected application. Then, investigate the update sets that these updates are in. If the Application field on these update sets does not contain a valid value, or if they are part of another application, they will not be cleaned up.
Usually, the updates are in the wrong update set due to being moved manually. It is strongly discouraged to move updates manually between update sets.
In order to resolve the issue and remove the changes from the Changed Files list, you must manually delete the sys_update_xml records for these files. Alternatively, you can move them into a valid update set that is part of the application, and then commit again to have the system clean them up.