If you change your repository configuration in particular by removing an old submodule, you may see an error message similar to the following when running a deployment:
ERROR: Repository not found. fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists. Stopping at 'path_to_submodule_here'; script returned non-zero status.
DeployHQ calculates changes using the commit references from your repository, so it may be attempting to run the deployment from a reference that no longer exists, as a result of removing the submodule.
You can resolve this issue simply by clicking the orange commit selection icon next the start commit reference, checking the option to Deploy the entire repository, then Select Commit.
You can see the Start Commit now reads Beginning of time.