You can delete all backups of specific folders from the Time Machine interface.

• Enter Time Machine (from the Time Machine menubar interface or from the Dock)
• Navigate to the /Library/Ruby/Gems/1.8/gems folder
• While the gems folder is selected, right click and choose Delete All Backups of <items(s)>
• Confirm that you wish to delete it and enter the Administrator credentials

See Should I delete old backups? If so, How? for more information and other ways to work with the AirPort Time Capsule.

You can delete all backups of specific folders from the Time Machine interface.

• Enter Time Machine (from the Time Machine menubar interface or from the Dock)
• Navigate to the /Library/Ruby/Gems/1.8/gems folder
• While the gems folder is selected, right click and choose Delete All Backups of <items(s)>
• Confirm that you wish to delete it and enter the Administrator credentials

If you have changed your machine's name after the reinstall, then Time Machine won't show your older backups. You can either rename your machine to the name it had before or press Option while clicking on the Time Machine menubar item and select Browse Other Backup Disks... to go through your backups.

See Should I delete old backups? If so, How? for more information and other ways to work with the AirPort Time Capsule.