The repository module uses 'templates' to format the output of the module. In fact, the repository module ships with a number different templates that allow you to use the module for different purposes by altering the format of the input/output.
Standard templates are stored in the /DesktopModules/Repository/Templates folder. And you use the module settings page to select which template you want to use.
So, for example, if you are using the filelist template, the module will use the files in the /DesktopModules/Repository/Templates/filelist folder.
HOWEVER, if you want to change a template, I suggest the following method to avoid having your changes overwritten on any module updates...
Example for changing the filelist template:
1. go to the root folder for the portal where you want to make the change and create a folder named RepositoryTemplates. eg: If you want to change the template in Portal 0, then create the following folder .. /Portals/0/RepositoryTemplates
2. create a folder with the same name as the template, in this case you would create a folder named /Portals/0/RepositoryTemplates/filelist
3. copy the files from /DesktopModules/Repository/Templates/filelist to /Portals/0/RepositoryTemplates/filelist
4. change the files in the /Portals/0/RepositoryTemplates/filelist folder.
Following that process will prevent your changes from being overwritten if you upgrade to a newer version of the repository module.
BTW: You can tell where your template is being loaded from on the module settings page, if the template name is preceeded with an asterisk, it means it's being loaded from the /Portals location and not the /DesktopModules location.