diff --git a/README.md b/README.md
index d358ea4..493d321 100644
--- a/README.md
+++ b/README.md
@@ -55,11 +55,11 @@ Docker images are not deleted though.
 
 # General Usage Information
 
-The `input` directory is for unprocessed publications as you might have received them from authors or editors.
-The `output` directory is for processed publications and intermediate data.
+The `runtime/input` directory is for unprocessed publications as you might have received them from authors or editors.
+The `runtime/output` directory is for processed publications and intermediate data.
 When entering the docker container conversion scripts are in your $PATH, and can executed like any other executable.
-In your `HOME` directory you'll find `input` and `output` directories, which are docker volumes mirroring the directories of the same name outside of the container.
-In order to compile a publication, just copy them into `./input`, enter the docker container, and call the necessary scripts.
+In your `HOME` directory you'll find `input` and `output` directories, which are docker volumes mirroring the directories in `runtime/` outside of the container.
+In order to compile a publication, just copy them into `runtime/input`, enter the docker container, and call the necessary scripts.
 For an example, see chapter "Workflows".
 
 ## Configuration
@@ -83,8 +83,8 @@ Compiling your documents involves following a workflow which can consist of seve
 
 ## The LaTeX workflow (eoatex -> pdf, django, epub)
 
-The following description uses the example publication in `input/example` (from the `eoa-publication-model` repository).
-In order to apply the workflow to any other publication copy it into the `input/` directory and adjust paths in the description accordingly.
+The following description uses the example publication in `runtime/input/example` (copied from the `eoa-publication-model` repository).
+In order to apply the workflow to any other publication copy it into the `runtime/input/` directory and adjust paths in the description accordingly.
 
 1. enter the docker container