diff --git a/src/bin/pegleg/pegleg/engine/lint.py b/src/bin/pegleg/pegleg/engine/lint.py
index b350008c..d5a4f84e 100644
--- a/src/bin/pegleg/pegleg/engine/lint.py
+++ b/src/bin/pegleg/pegleg/engine/lint.py
@@ -160,18 +160,31 @@ def _verify_document(document, schemas, filename):
 
 
 def _verify_deckhand_render(fail_on_missing_sub_src=False):
-    documents = []
+    sitenames = list(util.files.list_sites())
+    documents_by_site = {s: [] for s in sitenames}
 
-    for filename in util.files.all():
-        with open(filename) as f:
-            documents.extend(list(yaml.safe_load_all(f)))
+    for sitename in sitenames:
+        params = util.definition.load_as_params(sitename)
+        paths = util.files.directories_for(**params)
+        filenames = set(util.files.search(paths))
+        for filename in filenames:
+            with open(filename) as f:
+                documents_by_site[sitename].extend(list(yaml.safe_load_all(f)))
 
-    _, errors = util.deckhand.deckhand_render(
-        documents=documents,
-        fail_on_missing_sub_src=fail_on_missing_sub_src,
-        validate=True,
-    )
-    return errors
+    all_errors = []
+
+    for sitename, documents in documents_by_site.items():
+        LOG.debug('Rendering documents for site: %s.', sitename)
+        _, errors = util.deckhand.deckhand_render(
+            documents=documents,
+            fail_on_missing_sub_src=fail_on_missing_sub_src,
+            validate=True,
+        )
+        LOG.debug('Generated %d rendering errors for site: %s.', len(errors),
+                  sitename)
+        all_errors.extend(errors)
+
+    return list(set(all_errors))
 
 
 def _layer(data):
diff --git a/src/bin/pegleg/pegleg/engine/util/files.py b/src/bin/pegleg/pegleg/engine/util/files.py
index c2fd3e9a..3db8e8d7 100644
--- a/src/bin/pegleg/pegleg/engine/util/files.py
+++ b/src/bin/pegleg/pegleg/engine/util/files.py
@@ -104,6 +104,11 @@ def _create_tree(root_path, *, tree=FULL_STRUCTURE):
         os.makedirs(path, mode=0o775, exist_ok=True)
         _create_tree(path, tree=data)
 
+    for filename, yaml_data in tree.get('files', {}).items():
+        path = os.path.join(root_path, filename)
+        with open(path, 'w') as f:
+            yaml.safe_dump(yaml_data, f)
+
 
 def directories_for(*, site_name, revision, site_type):
     library_list = [
diff --git a/src/bin/pegleg/setup.py b/src/bin/pegleg/setup.py
index bdbec08f..53d15a5d 100644
--- a/src/bin/pegleg/setup.py
+++ b/src/bin/pegleg/setup.py
@@ -17,7 +17,7 @@ from setuptools import setup
 setup(
     name='pegleg',
     version='0.1.0',
-    packages=['pegleg'],
+    packages=['pegleg', 'tests'],
     entry_points={
         'console_scripts': [
             'pegleg=pegleg.cli:main',
diff --git a/src/bin/pegleg/tests/unit/engine/__init__.py b/src/bin/pegleg/tests/unit/engine/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/bin/pegleg/tests/unit/engine/test_lint.py b/src/bin/pegleg/tests/unit/engine/test_lint.py
new file mode 100644
index 00000000..5448b115
--- /dev/null
+++ b/src/bin/pegleg/tests/unit/engine/test_lint.py
@@ -0,0 +1,68 @@
+# Copyright 2018 AT&T Intellectual Property.  All other rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import mock
+
+from pegleg.engine import lint
+from pegleg.engine.util import files
+from tests.unit.fixtures import create_tmp_deployment_files
+
+
+def test_verify_deckhand_render_site_documents_separately(
+        create_tmp_deployment_files):
+    expected_documents = {
+        'cicd': [
+            'global-common', 'global-v1.0', 'cicd-type-common',
+            'cicd-type-v1.0', 'cicd-chart', 'cicd-passphrase'
+        ],
+        'lab': [
+            'global-common', 'global-v1.0', 'lab-type-common', 'lab-type-v1.0',
+            'lab-chart', 'lab-passphrase'
+        ],
+    }
+
+    with mock.patch(
+            'pegleg.engine.util.deckhand.deckhand_render',
+            autospec=True) as mock_render:
+        mock_render.return_value = (None, [])
+
+        result = lint._verify_deckhand_render()
+        assert result == []
+
+        sites = files.list_sites()
+
+        # Verify that both expected site types are listed.
+        assert sorted(sites) == ['cicd', 'lab']
+        # Verify that Deckhand called render twice, once for each site.
+        assert mock_render.call_count == 2
+
+        mock_calls = list(mock_render.mock_calls)
+        for mock_call in mock_calls:
+            documents = mock_call[2]['documents']
+            assert len(documents) == 7
+
+            # Verify one site_definition.yaml per site.
+            site_definitions = [x for x in documents if isinstance(x, dict)]
+            assert len(site_definitions) == 1
+
+            site_definition = site_definitions[0]
+            site_type = site_definition['data']['site_type']
+
+            assert site_definition['data']['revision'] == 'v1.0'
+            assert site_type in expected_documents
+
+            # Verify expected documents collected per site.
+            other_documents = expected_documents[site_type]
+            for other_document in other_documents:
+                assert other_document in documents
diff --git a/src/bin/pegleg/tests/unit/test_selectable_linting.py b/src/bin/pegleg/tests/unit/engine/test_selectable_linting.py
similarity index 100%
rename from src/bin/pegleg/tests/unit/test_selectable_linting.py
rename to src/bin/pegleg/tests/unit/engine/test_selectable_linting.py
diff --git a/src/bin/pegleg/tests/unit/engine/test_util_files.py b/src/bin/pegleg/tests/unit/engine/test_util_files.py
new file mode 100644
index 00000000..7c40de8c
--- /dev/null
+++ b/src/bin/pegleg/tests/unit/engine/test_util_files.py
@@ -0,0 +1,55 @@
+# Copyright 2018 AT&T Intellectual Property.  All other rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import tempfile
+
+from pegleg import config
+from pegleg.engine.util import files
+from tests.unit.fixtures import create_tmp_deployment_files
+
+
+def test_no_non_yamls(tmpdir):
+    p = tmpdir.mkdir("deployment_files").mkdir("global")
+    for x in range(3):  # Create 3 YAML files
+        p.join("good-%d.yaml" % x).write('fake-content')
+    p.join("bad.txt").write("fake-content")
+    config.set_primary_repo(str(tmpdir.listdir()[0]))
+    results = list(files.all())
+
+    assert 3 == len(results)
+    # Make sure only YAML files are returned
+    for i in results:
+        assert i.endswith('.yaml')
+
+
+def test_list_all_files(create_tmp_deployment_files):
+    expected_files = sorted([
+        'deployment_files/global/common/global-common.yaml',
+        'deployment_files/global/v1.0/global-v1.0.yaml',
+        'deployment_files/type/cicd/common/cicd-type-common.yaml',
+        'deployment_files/type/cicd/v1.0/cicd-type-v1.0.yaml',
+        'deployment_files/type/lab/common/lab-type-common.yaml',
+        'deployment_files/type/lab/v1.0/lab-type-v1.0.yaml',
+        'deployment_files/site/cicd/secrets/passphrases/cicd-passphrase.yaml',
+        'deployment_files/site/cicd/site-definition.yaml',
+        'deployment_files/site/cicd/software/charts/cicd-chart.yaml',
+        'deployment_files/site/lab/secrets/passphrases/lab-passphrase.yaml',
+        'deployment_files/site/lab/site-definition.yaml',
+        'deployment_files/site/lab/software/charts/lab-chart.yaml',
+    ])
+    actual_files = sorted(files.all())
+
+    assert len(actual_files) == len(expected_files)
+    for idx, file in enumerate(actual_files):
+        assert file.endswith(expected_files[idx])
diff --git a/src/bin/pegleg/tests/unit/fixtures.py b/src/bin/pegleg/tests/unit/fixtures.py
new file mode 100644
index 00000000..df7b2d49
--- /dev/null
+++ b/src/bin/pegleg/tests/unit/fixtures.py
@@ -0,0 +1,131 @@
+# Copyright 2018 AT&T Intellectual Property.  All other rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import absolute_import
+import os
+import tempfile
+
+import pytest
+import yaml
+
+from pegleg import config
+from pegleg.engine.util import files
+
+
+@pytest.fixture()
+def create_tmp_deployment_files(tmpdir):
+    """Fixture that creates a temporary directory structure."""
+    orig_primary_repo = config.get_primary_repo()
+    sitenames = ['cicd', 'lab']
+
+    SITE_TEST_STRUCTURE = {
+        'directories': {
+            'secrets': {
+                'directories': {
+                    'passphrases': {
+                        'files': {}
+                    },
+                },
+            },
+            'software': {
+                'directories': {
+                    'charts': {
+                        'files': {}
+                    },
+                },
+            },
+        },
+        'files': {}
+    }
+
+    p = tmpdir.mkdir("deployment_files")
+    config.set_primary_repo(str(p))
+
+    # Create global directories and files.
+    files._create_tree(
+        os.path.join(str(p), 'global'),
+        tree={
+            'directories': {
+                'common': {
+                    'files': {
+                        'global-common.yaml': 'global-common'
+                    }
+                },
+                'v1.0': {
+                    'files': {
+                        'global-v1.0.yaml': 'global-v1.0'
+                    }
+                }
+            }
+        })
+
+    # Create type directories and files.
+    files._create_tree(
+        os.path.join(str(p), 'type'),
+        tree={
+            'directories': {
+                site: {
+                    'directories': {
+                        'common': {
+                            'files': {
+                                '%s-type-common.yaml' % site:
+                                ('%s-type-common' % site)
+                            }
+                        },
+                        'v1.0': {
+                            'files': {
+                                '%s-type-v1.0.yaml' % site:
+                                ('%s-type-v1.0' % site)
+                            }
+                        }
+                    }
+                }
+                for site in sitenames
+            }
+        })
+
+    # Create site directories and files.
+    for site in sitenames:
+        site_definition = """
+---
+data:
+  revision: v1.0
+  site_type: %s
+metadata:
+  layeringDefinition: {abstract: false, layer: site}
+  name: %s
+  schema: metadata/Document/v1
+  storagePolicy: cleartext
+schema: pegleg/SiteDefinition/v1
+...
+""" % (site, site)
+
+        test_structure = SITE_TEST_STRUCTURE.copy()
+        test_structure['directories']['secrets']['directories']['passphrases'][
+            'files'] = {
+                '%s-passphrase.yaml' % site: '%s-passphrase' % site
+            }
+        test_structure['directories']['software']['directories']['charts'][
+            'files'] = {
+                '%s-chart.yaml' % site: '%s-chart' % site
+            }
+        test_structure['files']['site-definition.yaml'] = yaml.safe_load(
+            site_definition)
+
+        cicd_path = os.path.join(str(p), files._site_path(site))
+        files._create_tree(cicd_path, tree=test_structure)
+
+    yield
+
+    config.set_primary_repo(orig_primary_repo)
diff --git a/src/bin/pegleg/tests/unit/test_engine_util_files.py b/src/bin/pegleg/tests/unit/test_engine_util_files.py
deleted file mode 100644
index 7a5b1ea8..00000000
--- a/src/bin/pegleg/tests/unit/test_engine_util_files.py
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 2018 AT&T Intellectual Property.  All other rights reserved.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-import tempfile
-
-from pegleg import config
-from pegleg.engine.util import files
-
-
-def test_no_non_yamls(tmpdir):
-    p = tmpdir.mkdir("site_yamls").mkdir("global")
-    for x in range(3):  # Create 3 YAML files
-        p.join("good-%d.yaml" % x).write('fake-content')
-    p.join("bad.txt").write("fake-content")
-    config.set_primary_repo(str(tmpdir.listdir()[0]))
-    results = list(files.all())
-
-    assert 3 == len(results)
-    # Make sure only YAML files are returned
-    for i in results:
-        assert i.endswith('.yaml')
diff --git a/src/bin/pegleg/tox.ini b/src/bin/pegleg/tox.ini
index 0658b6a4..c6795d50 100644
--- a/src/bin/pegleg/tox.ini
+++ b/src/bin/pegleg/tox.ini
@@ -28,4 +28,4 @@ commands =
     flake8 {toxinidir}/pegleg
 
 [flake8]
-ignore = E251,W503
+ignore = E125,E251,W503