chore: restructure deployement stuff

Makefile

@@ -6,7 +6,7 @@ PYTHON_CMD := $(shell command -v python3 2> /dev/null)
 BUILDAH_CMD := $(shell command -v buildah 2> /dev/null)
 DOCKER_CMD := $(shell command -v docker 2> /dev/null)
 ELIXIR_CLOUD_REGISTRY := docker.io/elixircloud
-DOCKER_FILE_PATH := containers
+DOCKER_FILE_PATH := deployment/containers
 
 # Define arguments
 IMAGE ?= filer

README.md

@@ -1,7 +1,7 @@
-<img src="documentation/img/TESKlogowfont.png" height="200">
+<img src="deployment/documentation/img/TESKlogowfont.png" height="200">
 
 
-An implementation of a task execution engine based on the [TES standard](https://github.com/ga4gh/task-execution-schemas) running on `Kubernetes`. For more details on `TES`, see the (very) brief [introduction to TES](documentation/tesintro.md).
+An implementation of a task execution engine based on the [TES standard](https://github.com/ga4gh/task-execution-schemas) running on `Kubernetes`. For more details on `TES`, see the (very) brief [introduction to TES](deployment/documentation/tesintro.md).
 
 For organisational reasons, this project is split into 3 repositories:
 - This one, which contains documentation and deployment files
@@ -10,15 +10,16 @@ For organisational reasons, this project is split into 3 repositories:
 
 If the API is running on your cluster it will pull the images from our `docker.io` repository automatically.
 
-`TESK` is designed with the goal to support any `Kubernetes` cluster, for its deployment please refer to the [deployment](documentation/deployment.md) page.
+`TESK` is designed with the goal to support any `Kubernetes` cluster, for its deployment please refer to the [deployment](deployment/documentation/deployment.md) page.
 
-The technical documentation is available in the [documentation](documentation) folder.
+The technical documentation is available in the [documentation](deployment/documentation) folder.
 
 
 ## Architecture
 As a diagram:
 
-![TESK architecture](documentation/img/architecture.png)
+# TODO: Change the image remove tomcat, change naming etc
+![TESK architecture](deployment/documentation/img/architecture.png)
 
 **Description**: The first pod in the task lifecycle is the API pod, a pod which runs a web server (`Tomcat`) and exposes the `TES` specified endpoints. It consumes `TES` requests, validates them and translates them to `Kubernetes` jobs. The API pod then creates a `task controller` pod, or `taskmaster`. 
 
@@ -30,4 +31,4 @@ After the last executor, the `filer` is called once more to process the outputs
 -   A working [Kubernetes](https://kubernetes.io/) cluster version 1.9 and later.
 -   If you want TESK to handle tasks with I/O (and you probably want), you additionally need:
 -   A default storage class, which TESK will use to create temporary PVCs. It is enough that the storage class supports the RWO mode.
--   And, if you want TESK to integrate with workflow managers, you additionally need either an FTP account or a PVC that can be accessed from within or from outside of the cluster by the workflow manager (more in the [deployment](documentation/deployment.md) page).
+-   And, if you want TESK to integrate with workflow managers, you additionally need either an FTP account or a PVC that can be accessed from within or from outside of the cluster by the workflow manager (more in the [deployment](deployment/documentation/deployment.md) page).