Step 1: Reorganize folder structure

[yanniszark]

Part-of: #1735

Currently, the manifests repo is a flat namespace with everything mangled.
We plan to reorganize the folder structure into sections that will reflect the
following properties:

• Applications with their source code in upstream KF maintained by Kubeflow WGs (e.g., notebook-controller)
• Common services (Dex, Istio, Cert-Manager, KNative), maintained by the
  Manifests WG.
• Applications contributed by community members, not owned by any Kubeflow WG.
• Distribution-specific manifests (kfdef, stacks, aws, gcp, etc.). The goal is
  for this folder to become empty in subsequent releases.

BEFORE (folders only):

.
├── admission-webhook
├── application
├── argo
├── aws
├── cert-manager
├── common
├── default-install
├── dex-auth
├── docs
├── experimental
├── flink
├── gatekeeper
├── gcp
├── hack
├── istio
├── istio-1-3-1
├── jupyter
├── katib
├── kfdef
├── kfserving
├── knative
├── kubebench
├── kubeflow-roles
├── metacontroller
├── metadata
├── modeldb
├── mpi-job
├── mxnet-job
├── namespaces
├── pipeline
├── profiles
├── pytorch-job
├── seldon
├── spark
├── stacks
├── tektoncd
├── tests
├── tf-training
└── xgboost-job

AFTER (folders only):

.
├── apps
│   ├── admission-webhook/upstream
│   ├── centraldashboard/upstream
│   ├── jupyter/jupyter-web-app/upstream
│   ├── jupyter/notebook-controller/upstream
│   ├── katib/upstream
│   ├── kfserving/upstream
│   ├── kubebench/upstream
│   ├── mpi-job/upstream
│   ├── mxnet-job/upstream
│   ├── pipeline/upstream
│   ├── profiles/upstream
│   ├── pytorch-job/upstream
│   ├── tf-training/upstream
│   └── xgboost-job/upstream
├── common
│   ├── cert-manager
│   ├── dex-auth
│   ├── istio
│   ├── istio-1-3-1
│   ├── knative
│   ├── kubeflow-roles
│   └── namespaces
├── contrib
│   ├── application
│   ├── argo
│   ├── basic-auth
│   ├── default-install
│   ├── experimental
│   ├── flink
│   ├── gatekeeper
│   ├── metacontroller
│   ├── metadata
│   ├── modeldb
│   ├── seldon
│   ├── spark
│   ├── spartakus
│   └── tektoncd
├── distributions
│   ├── aws
│   ├── gcp
│   ├── kfdef
│   └── stacks
├── docs
├── hack
└── tests