diff --git a/cli/engine/ApplyEngine.py b/cli/engine/ApplyEngine.py
index 836b0e4265..7dbbe4c090 100644
--- a/cli/engine/ApplyEngine.py
+++ b/cli/engine/ApplyEngine.py
@@ -1,13 +1,10 @@
 import os
 import sys
 
-from ansible.parsing.dataloader import DataLoader
-from ansible.inventory.manager import InventoryManager
-
 from cli.version import VERSION
 from cli.helpers.Step import Step
 from cli.helpers.doc_list_helpers import select_single, select_all, select_first
-from cli.helpers.build_io import save_manifest, load_manifest, get_inventory_path, get_manifest_path, get_build_path
+from cli.helpers.build_io import save_manifest, load_manifest, get_inventory_path, get_manifest_path, get_build_path, load_inventory
 from cli.helpers.yaml_helpers import safe_load_all
 from cli.helpers.Log import Log
 from cli.helpers.os_images import get_os_distro_normalized
@@ -39,7 +36,7 @@ def __init__(self, input_data):
         self.infrastructure_docs = []
         self.manifest_docs = []
 
-        self.__ping_retries: int = input_data.ping_retries
+        self.ping_retries: int = input_data.ping_retries
 
     def __enter__(self):
         return self
@@ -121,7 +118,7 @@ def assert_no_master_downscale(self):
         inventory_path = get_inventory_path(cluster_name)
 
         if os.path.isfile(inventory_path):
-            existing_inventory = InventoryManager(loader=DataLoader(), sources=inventory_path)
+            existing_inventory = load_inventory(inventory_path)
 
             both_present = all([
                 'kubernetes_master' in existing_inventory.list_groups(),
@@ -149,7 +146,7 @@ def assert_no_postgres_nodes_number_change(self):
 
         if os.path.isfile(inventory_path):
             next_postgres_node_count = 0
-            existing_inventory = InventoryManager(loader=DataLoader(), sources=inventory_path)
+            existing_inventory = load_inventory(inventory_path)
             prev_postgres_node_count = len(existing_inventory.list_hosts(pattern='postgresql'))
             postgres_available = [x for x in feature_mapping.specification.available_roles if x.name == 'postgresql']
             if postgres_available[0].enabled:
@@ -196,7 +193,7 @@ def apply(self):
 
         self.assert_consistent_os_family()
 
-        if not (self.skip_infrastructure or self.is_provider_any(self.cluster_model)):
+        if not (self.skip_infrastructure or self.cluster_model['provider'] == 'any'):
             # Generate terraform templates
             with TerraformTemplateGenerator(self.cluster_model, self.infrastructure_docs) as template_generator:
                 template_generator.run()
@@ -222,19 +219,7 @@ def apply(self):
         # Run Ansible to provision infrastructure
         if not(self.skip_config):
             with AnsibleRunner(self.cluster_model, docs, ansible_options=self.ansible_options,
-                               ping_retries=self.__ping_retries) as ansible_runner:
+                               ping_retries=self.ping_retries) as ansible_runner:
                 ansible_runner.apply()
 
         return 0
-
-    def dry_run(self):
-
-        self.process_input_docs()
-
-        self.process_configuration_docs()
-
-        return [*self.configuration_docs, *self.infrastructure_docs]
-
-    @staticmethod
-    def is_provider_any(cluster_model):
-        return cluster_model["provider"] == "any"
diff --git a/cli/engine/InitEngine.py b/cli/engine/InitEngine.py
index 3f021f78a9..3a9efe62c4 100644
--- a/cli/engine/InitEngine.py
+++ b/cli/engine/InitEngine.py
@@ -3,10 +3,11 @@
 from cli.helpers.Step import Step
 from cli.helpers.build_io import save_manifest, get_build_path
 from cli.helpers.data_loader import load_all_schema_objs, types
-from cli.engine.ApplyEngine import ApplyEngine
 from cli.helpers.objdict_helpers import remove_value
 from cli.version import VERSION
-from cli.helpers.doc_list_helpers import select_all, select_single
+from cli.helpers.doc_list_helpers import select_all
+from cli.engine.schema.ConfigurationAppender import ConfigurationAppender
+from cli.engine.schema.DefaultMerger import DefaultMerger
 
 
 class InitEngine(Step):
@@ -25,23 +26,29 @@ def __exit__(self, exc_type, exc_value, traceback):
         pass
 
     def init(self):
-        input = load_all_schema_objs(types.DEFAULT, self.provider, 'configuration/minimal-cluster-config')
-        input[0].specification.name = self.name
+        # Load the minimal cluster-config doc and set the cluster name
+        docs = load_all_schema_objs(types.DEFAULT, self.provider, 'configuration/minimal-cluster-config')
+        docs[0].specification.name = self.name
 
+        # For full we also add the infrastructure and configuration documents
         if self.is_full_config:
-            config = self.get_config_docs(input)
-            config_only = select_all(config, lambda x: not(x.kind.startswith('epiphany-cluster')))
-            if self.provider == 'any':
-                # for any provider we want to use the default config from minimal-cluster-config
-                cluster_model = select_single(input, lambda x: x.kind == 'epiphany-cluster')
+            # Merge with defaults
+            with DefaultMerger(docs) as doc_merger:
+                    docs = doc_merger.run()
+
+            # Add infrastructure and configuration documents
+            if self.provider != 'any':
+                # Add VM infrastructure docs as these are most likely to be changed
+                infra_docs = load_all_schema_objs(types.DEFAULT, self.provider, 'infrastructure/virtual-machine')
             else:
-                # for azure|aws provider we want to use the extended defaults cluster-config after dry run.
-                # TODO: We probably wants this comming from seperate documents since Azure and AWS overlap now...
-                cluster_model = select_single(config, lambda x: x.kind == 'epiphany-cluster')
-            infra  = self.get_infra_docs(input)
-            docs = [cluster_model, *config_only, *infra]
-        else:
-            docs = [*input]
+                # For any provider, infrastructure docs are already part of the minimal-cluster-config template
+                infra_docs = select_all(docs, lambda x: x.kind.startswith('infrastructure/machine'))
+
+            # Add configuration documents
+            with ConfigurationAppender(docs) as config_appender:
+                config_docs = config_appender.run()
+
+            docs = [*config_docs, *infra_docs]
 
         # set the provider and version for all docs
         for doc in docs:
@@ -52,35 +59,7 @@ def init(self):
         remove_value(docs, 'SET_BY_AUTOMATION')
 
         # save document
-        save_manifest(docs, self.name, self.name+'.yml')
+        save_manifest(docs, self.name, f'{ self.name }.yml')
 
         self.logger.info('Initialized new configuration and saved it to "' + os.path.join(get_build_path(self.name), self.name + '.yml') + '"')
         return 0
-
-    def get_config_docs(self, input_docs):
-        cluster_config_path = save_manifest(input_docs, self.name, self.name + '.yml')
-        args = type('obj', (object,), {'file': cluster_config_path})()
-        args.ansible_forks = 10  # TODO: remove these workarounds
-        args.ping_retries = 5
-
-        # generate the config documents
-        with ApplyEngine(args) as build:
-            config = build.dry_run()
-
-        return config
-
-    def get_infra_docs(self, input_docs):
-        if self.provider == 'any':
-            # For any we can include the machine documents from the minimal-cluster-config
-            infra = select_all(input_docs, lambda x: x.kind.startswith('infrastructure/machine'))
-        else:
-            # VMs are curently the infrastructure documents the user might interact with for:
-            # - type/size
-            # - distro
-            # - network security rules
-            # ...
-            # So we add the defaults here.
-            # TODO: Check if we want to include possible other infrastructure documents.
-            infra = load_all_schema_objs(types.DEFAULT, self.provider, 'infrastructure/virtual-machine')
-
-        return infra
diff --git a/cli/engine/UpgradeEngine.py b/cli/engine/UpgradeEngine.py
index 0fc7bad0df..5754eb6195 100644
--- a/cli/engine/UpgradeEngine.py
+++ b/cli/engine/UpgradeEngine.py
@@ -21,7 +21,7 @@ def __init__(self, input_data):
         self.backup_build_dir = ''
         self.ansible_command = AnsibleCommand()
         self.input_docs = []
-        self.__ping_retries: int = input_data.ping_retries
+        self.ping_retries: int = input_data.ping_retries
 
     def __enter__(self):
         super().__enter__()
@@ -88,7 +88,7 @@ def upgrade(self):
         # Run Ansible to upgrade infrastructure
         with AnsibleRunner(build_dir=self.build_dir, backup_build_dir=self.backup_build_dir,
                            ansible_options=self.ansible_options, config_docs=self.input_docs,
-                           ping_retries=self.__ping_retries) as ansible_runner:
+                           ping_retries=self.ping_retries) as ansible_runner:
             ansible_runner.upgrade()
 
         return 0
diff --git a/cli/engine/ansible/AnsibleInventoryUpgrade.py b/cli/engine/ansible/AnsibleInventoryUpgrade.py
index 67ddc5a515..61e8a3085c 100644
--- a/cli/engine/ansible/AnsibleInventoryUpgrade.py
+++ b/cli/engine/ansible/AnsibleInventoryUpgrade.py
@@ -1,12 +1,8 @@
-from ansible.parsing.dataloader import DataLoader
-from ansible.inventory.manager import InventoryManager
-
 from cli.helpers.Step import Step
 from cli.helpers.build_io import get_inventory_path_for_build
 from cli.models.AnsibleHostModel import AnsibleHostModel
 from cli.models.AnsibleInventoryItem import AnsibleInventoryItem
-from cli.helpers.build_io import save_inventory, load_manifest
-from cli.helpers.objdict_helpers import dict_to_objdict
+from cli.helpers.build_io import save_inventory, load_manifest, load_inventory
 from cli.helpers.data_loader import load_schema_obj, types as data_types
 from cli.helpers.doc_list_helpers import select_single
 from cli.helpers.objdict_helpers import merge_objdict
@@ -56,7 +52,7 @@ def upgrade(self):
         inventory_path = get_inventory_path_for_build(self.backup_build_dir)
 
         self.logger.info(f'Loading backup Ansible inventory: {inventory_path}')
-        loaded_inventory = InventoryManager(loader = DataLoader(), sources=inventory_path)
+        loaded_inventory = load_inventory(inventory_path)
 
         # move loaded inventory to templating structure
         new_inventory = []
diff --git a/cli/engine/ansible/AnsibleRunner.py b/cli/engine/ansible/AnsibleRunner.py
index eaff61ca7d..58ada62606 100644
--- a/cli/engine/ansible/AnsibleRunner.py
+++ b/cli/engine/ansible/AnsibleRunner.py
@@ -27,7 +27,7 @@ def __init__(self, cluster_model=None, config_docs=None, build_dir=None, backup_
         self.backup_build_dir = backup_build_dir
         self.ansible_options = ansible_options
         self.ansible_command = AnsibleCommand()
-        self.__ping_retries: int = ping_retries
+        self.ping_retries: int = ping_retries
 
     def __enter__(self):
         super().__enter__()
@@ -57,7 +57,7 @@ def pre_flight(self, inventory_path):
         self.ansible_command.run_task_with_retries(inventory=inventory_path,
                                                    module="ping",
                                                    hosts="all",
-                                                   retries=self.__ping_retries)
+                                                   retries=self.ping_retries)
 
         self.logger.info('Checking preflight conditions on each machine')
         self.ansible_command.run_playbook_with_retries(inventory=inventory_path,
@@ -106,7 +106,6 @@ def apply(self):
         # create inventory
         inventory_creator = AnsibleInventoryCreator(self.cluster_model, self.config_docs)
         inventory_creator.create()
-        time.sleep(10)
 
         # create ansible.cfg
         ansible_config_file_path = get_ansible_config_file_path(self.cluster_model.specification.name)
diff --git a/cli/engine/schema/ConfigurationAppender.py b/cli/engine/schema/ConfigurationAppender.py
index 3f0f92dc74..d8b76ec554 100644
--- a/cli/engine/schema/ConfigurationAppender.py
+++ b/cli/engine/schema/ConfigurationAppender.py
@@ -7,7 +7,7 @@
 
 
 class ConfigurationAppender(Step):
-    REQUIRED_DOCS = ['configuration/feature-mapping', 'configuration/shared-config', 'epiphany-cluster']
+    REQUIRED_DOCS = ['epiphany-cluster', 'configuration/feature-mapping', 'configuration/shared-config']
 
     def __init__(self, input_docs):
         super().__init__(__name__)
diff --git a/cli/epicli.py b/cli/epicli.py
index aaca209adf..c32610ae1a 100644
--- a/cli/epicli.py
+++ b/cli/epicli.py
@@ -490,9 +490,7 @@ def dump_external_debug_info(title, args):
         dump_file.write('\n\n*****PYTHON******\n')
         dump_file.write(f'python_version: {platform.python_version()}\n')
         dump_file.write(f'python_build: {platform.python_build()}\n')
-        dump_file.write(f'python_revision: {platform.python_revision()}\n')
         dump_file.write(f'python_compiler: {platform.python_compiler()}\n')
-        dump_file.write(f'python_branch: {platform.python_branch()}\n')
         dump_file.write(f'python_implementation: {platform.python_implementation()}\n')
 
         dump_external_debug_info('ANSIBLE VERSION', ['ansible', '--version'])
@@ -501,7 +499,7 @@ def dump_external_debug_info(title, args):
         dump_external_debug_info('TERRAFORM VERSION', ['terraform', '--version'])
         dump_external_debug_info('RUBY VERSION', ['ruby', '--version'])
         dump_external_debug_info('RUBY GEM VERSION', ['gem', '--version'])
-        dump_external_debug_info('RUBY INSTALLED GEMS', ['gem', 'query', '--local'])
+        dump_external_debug_info('RUBY INSTALLED GEMS', ['gem', 'list', '--local'])
 
         dump_file.write('\n\n*****LOG******\n')
         log_path = os.path.join(get_output_path(), config.log_file)
diff --git a/cli/helpers/build_io.py b/cli/helpers/build_io.py
index 0001851980..6f6efa076e 100644
--- a/cli/helpers/build_io.py
+++ b/cli/helpers/build_io.py
@@ -5,6 +5,9 @@
 from os.path import isfile, join
 from distutils import dir_util
 
+from ansible.parsing.dataloader import DataLoader
+from ansible.inventory.manager import InventoryManager
+
 from cli.helpers.data_loader import load_template_file, load_yamls_file, types
 from cli.helpers.yaml_helpers import dump_all, dump
 from cli.helpers.Config import Config
@@ -53,6 +56,10 @@ def save_inventory(inventory, cluster_model, build_dir=None):
     save_to_file(file_path, content)
 
 
+def load_inventory(inventory_path):
+    return InventoryManager(loader=DataLoader(), sources=inventory_path)
+
+
 def save_ansible_config_file(ansible_config_file_settings, ansible_config_file_path):
     template = load_template_file(types.ANSIBLE, '', ANSIBLE_CFG_FILE)
     content = template.render(ansible_config_file_settings=ansible_config_file_settings)
diff --git a/docs/changelogs/CHANGELOG-2.0.md b/docs/changelogs/CHANGELOG-2.0.md
index d886942d14..4cc4dfd66c 100644
--- a/docs/changelogs/CHANGELOG-2.0.md
+++ b/docs/changelogs/CHANGELOG-2.0.md
@@ -14,8 +14,9 @@
 - [#1569](https://github.com/epiphany-platform/epiphany/issues/1569) - Azure unmanaged disks not supported by Epiphany but there is misleading setting in the default configuration
 - [#2832](https://github.com/epiphany-platform/epiphany/issues/2832) - Make the DoD checklist clear
 - [#2853](https://github.com/epiphany-platform/epiphany/issues/2853) - Change autoscaling_group approach in AWS provider in favor of plain VM creation.
-
 - [#2669](https://github.com/epiphany-platform/epiphany/issues/2669) - Restarting the installation process can cause certificate problems if K8s was not fully configured
+- [#2944](https://github.com/epiphany-platform/epiphany/issues/2944) - Refactor InitEngine class to be agnostic to changes in ApplyEngine and UpgradeEngine
+- [#2945](https://github.com/epiphany-platform/epiphany/issues/2945) - epicli apply sleeps 10 seconds after creating inventory
 
 ### Updated
 
diff --git a/schema/any/defaults/epiphany-cluster.yml b/schema/any/defaults/epiphany-cluster.yml
index 4bc8719823..27a3014ac2 100644
--- a/schema/any/defaults/epiphany-cluster.yml
+++ b/schema/any/defaults/epiphany-cluster.yml
@@ -11,45 +11,45 @@ specification:
   components:
     kubernetes_master:
       count: 1
-      machine: kubernetes-master-machine
+      machines: []
       configuration: default
     kubernetes_node:
       count: 2
-      machine: kubernetes-node-machine
+      machines: []
       configuration: default
     logging:
       count: 1
-      machine: logging-machine
+      machines: []
       configuration: default
     monitoring:
       count: 1
-      machine: monitoring-machine
+      machines: []
       configuration: default
     kafka:
       count: 2
-      machine: kafka-machine
+      machines: []
       configuration: default
     postgresql:
       count: 0
-      machine: postgresql-machine
+      machines: []
       configuration: default
     load_balancer:
       count: 1
-      machine: load-balancer-machine
+      machines: []
       configuration: default
     rabbitmq:
       count: 0
-      machine: rabbitmq-machine
+      machines: []
       configuration: default
     opendistro_for_elasticsearch:
       count: 0
-      machine: logging-machine
+      machines: []
       configuration: default
     repository:
       count: 1
-      machine: repository-machine
+      machines: []
       configuration: default
     single_machine:
       count: 0
-      machine: single-machine
+      machines: []
       configuration: default