Could it be, that the repo_folder option in the file acceptance.suite.yml is not actively used. If you search for the word repo_folder, there are only hits in the _Data directory. Afaik this directory is just there to store test data. For example, I'm testing the upload of a GPX File. For this I put the GPX file in the directory _Data and here it is found with the function attachFile() (http://codeception.com/docs/modules/WebDriver#attachFile). Or you can save a dump of a database here and read this dump before each test.
Also the description for the option repo_folder does not fit. The description is "# Path to the Extension repository. To be used by install to install via folder ". However, there is no active test that installs web links from a directory. Afaik there is only one test who installs web links from a URL.
Can we delete the option repo_folder and the data in the _Data directory?