diff --git a/doc/source/reference/job_def.rst b/doc/source/reference/job_def.rst
index e509a9b873..36ad98ea56 100644
--- a/doc/source/reference/job_def.rst
+++ b/doc/source/reference/job_def.rst
@@ -866,3 +866,36 @@ Here is an example of two job definitions:
       This means that changes to jobs with file matchers will be
       self-testing without requiring that the file matchers include
       the Zuul configuration file defining the job.
+
+   .. attr:: workspace-scheme
+      :default: golang
+
+      The scheme to use when placing git repositories in the
+      workspace.
+
+      .. value:: golang
+
+         This writes the repository into a directory based on the
+         canonical hostname and the full name of the repository.  For
+         example::
+
+           src/example.com/organization/project
+
+         This is the default and, despite the name, is suitable and
+         recommended for any language.
+
+      .. value:: flat
+
+         This writes the repository into a directory based only on the
+         last component of the name.  For example::
+
+           src/project
+
+         In some cases the ``golang`` scheme can produce collisions
+         (conisder the projects `component` and
+         `component/subcomponent`).  In this case it may be preferable
+         to use the ``flat`` scheme (which would produce repositories
+         at `component` and `subcomponent`).
+
+         Note, however, that this scheme may produce collisions with
+         `component` and `component/component`.
diff --git a/releasenotes/notes/workspace-scheme-277215ff2c6fd4af.yaml b/releasenotes/notes/workspace-scheme-277215ff2c6fd4af.yaml
new file mode 100644
index 0000000000..73e7ad2d80
--- /dev/null
+++ b/releasenotes/notes/workspace-scheme-277215ff2c6fd4af.yaml
@@ -0,0 +1,15 @@
+---
+features:
+  - |
+    Jobs may now specify an alternate scheme to use when preparing
+    repositories in the workspace.  The default remains the same
+    golang-style, but an alternate scheme called `flat` is now
+    available.  See :attr:`job.workspace-scheme` for more details.
+upgrade:
+  - |
+    The internal git repo caches maintained by the mergers and
+    executors now use a new naming scheme in order to avoid
+    collisions.  When existing executors and mergers are restarted,
+    they will remove their git repo caches and re-clone repos using
+    the new scheme.  Jobs may be slow to start until the caches are
+    warmed again.
diff --git a/tests/fixtures/layouts/overlapping-repos.yaml b/tests/fixtures/layouts/overlapping-repos.yaml
new file mode 100644
index 0000000000..3fb68b81b0
--- /dev/null
+++ b/tests/fixtures/layouts/overlapping-repos.yaml
@@ -0,0 +1,65 @@
+- pipeline:
+    name: check
+    manager: independent
+    trigger:
+      gerrit:
+        - event: patchset-created
+    success:
+      gerrit:
+        Verified: 1
+    failure:
+      gerrit:
+        Verified: -1
+
+- pipeline:
+    name: gate
+    manager: dependent
+    success-message: Build succeeded (gate).
+    trigger:
+      gerrit:
+        - event: comment-added
+          approval:
+            - Approved: 1
+    success:
+      gerrit:
+        Verified: 2
+        submit: true
+    failure:
+      gerrit:
+        Verified: -2
+    start:
+      gerrit:
+        Verified: 0
+    precedence: high
+
+- pipeline:
+    name: post
+    manager: independent
+    trigger:
+      gerrit:
+        - event: ref-updated
+          ref: ^(?!refs/).*$
+
+- job:
+    name: base
+    parent: null
+    run: playbooks/base.yaml
+
+- job:
+    name: test-job
+    workspace-scheme: flat
+    required-projects:
+      - component/subcomponent
+      - component
+
+- project:
+    name: component/subcomponent
+    check:
+      jobs:
+        - test-job
+
+- project:
+    name: component
+    check:
+      jobs:
+        - test-job
diff --git a/tests/unit/test_merger_repo.py b/tests/unit/test_merger_repo.py
index bdd00b2314..31a72171f5 100644
--- a/tests/unit/test_merger_repo.py
+++ b/tests/unit/test_merger_repo.py
@@ -20,9 +20,9 @@ import os
 import git
 import testtools
 
-from zuul.merger.merger import Repo
-from zuul.model import MERGER_MERGE_RESOLVE
-from tests.base import ZuulTestCase, FIXTURE_DIR, simple_layout
+from zuul.merger.merger import MergerTree, Repo
+import zuul.model
+from tests.base import BaseTestCase, ZuulTestCase, FIXTURE_DIR, simple_layout
 
 
 class TestMergerRepo(ZuulTestCase):
@@ -701,7 +701,7 @@ class TestMerger(ZuulTestCase):
             branch=fake_change.branch,
             project=fake_change.project,
             buildset_uuid='fake-uuid',
-            merge_mode=MERGER_MERGE_RESOLVE,
+            merge_mode=zuul.model.MERGER_MERGE_RESOLVE,
         )
 
     def test_merge_multiple_items(self):
@@ -913,7 +913,7 @@ class TestMerger(ZuulTestCase):
 
         # Add an index.lock file
         fpath = os.path.join(self.merger_src_root, 'review.example.com',
-                             'org', 'project1', '.git', 'index.lock')
+                             'org', 'org%2Fproject1', '.git', 'index.lock')
         with open(fpath, 'w'):
             pass
         self.assertTrue(os.path.exists(fpath))
@@ -1003,3 +1003,163 @@ class TestMerger(ZuulTestCase):
                          zuul_repo.commit('refs/heads/master').hexsha)
         self.assertEqual(upstream_repo.commit(change_ref).hexsha,
                          zuul_repo.commit('HEAD').hexsha)
+
+
+class TestMergerTree(BaseTestCase):
+
+    def test_tree(self):
+        t = MergerTree()
+
+        t.add('/root/component')
+        t.add('/root/component2')
+        with testtools.ExpectedException(Exception):
+            t.add('/root/component/subcomponent')
+        t.add('/root/foo/bar/baz')
+        with testtools.ExpectedException(Exception):
+            t.add('/root/foo')
+
+
+class TestMergerSchemes(ZuulTestCase):
+    tenant_config_file = 'config/single-tenant/main.yaml'
+
+    def setUp(self):
+        super().setUp()
+        self.work_root = os.path.join(self.test_root, 'workspace')
+        self.cache_root = os.path.join(self.test_root, 'cache')
+
+    def _getMerger(self, work_root=None, cache_root=None, scheme=None):
+        work_root = work_root or self.work_root
+        return self.executor_server._getMerger(
+            work_root, cache_root=cache_root, scheme=scheme)
+
+    def _assertScheme(self, root, scheme):
+        if scheme == 'unique':
+            self.assertTrue(os.path.exists(
+                os.path.join(root, 'review.example.com',
+                             'org/org%2Fproject1')))
+        else:
+            self.assertFalse(os.path.exists(
+                os.path.join(root, 'review.example.com',
+                             'org/org%2Fproject1')))
+
+        if scheme == 'golang':
+            self.assertTrue(os.path.exists(
+                os.path.join(root, 'review.example.com',
+                             'org/project1')))
+        else:
+            self.assertFalse(os.path.exists(
+                os.path.join(root, 'review.example.com',
+                             'org/project1')))
+
+        if scheme == 'flat':
+            self.assertTrue(os.path.exists(
+                os.path.join(root, 'project1')))
+        else:
+            self.assertFalse(os.path.exists(
+                os.path.join(root, 'project1')))
+
+    def test_unique_scheme(self):
+        merger = self._getMerger(scheme=zuul.model.SCHEME_UNIQUE)
+        merger.getRepo('gerrit', 'org/project1')
+        self._assertScheme(self.work_root, 'unique')
+
+    def test_golang_scheme(self):
+        cache_merger = self._getMerger(work_root=self.cache_root)
+        cache_merger.updateRepo('gerrit', 'org/project1')
+        self._assertScheme(self.cache_root, 'unique')
+
+        merger = self._getMerger(
+            cache_root=self.cache_root,
+            scheme=zuul.model.SCHEME_GOLANG)
+        merger.getRepo('gerrit', 'org/project1')
+        self._assertScheme(self.work_root, 'golang')
+
+    def test_flat_scheme(self):
+        cache_merger = self._getMerger(work_root=self.cache_root)
+        cache_merger.updateRepo('gerrit', 'org/project1')
+        self._assertScheme(self.cache_root, 'unique')
+
+        merger = self._getMerger(
+            cache_root=self.cache_root,
+            scheme=zuul.model.SCHEME_FLAT)
+        merger.getRepo('gerrit', 'org/project1')
+        self._assertScheme(self.work_root, 'flat')
+
+    @simple_layout('layouts/overlapping-repos.yaml')
+    def test_golang_collision(self):
+        merger = self._getMerger(scheme=zuul.model.SCHEME_GOLANG)
+        repo = merger.getRepo('gerrit', 'component')
+        self.assertIsNotNone(repo)
+        repo = merger.getRepo('gerrit', 'component/subcomponent')
+        self.assertIsNone(repo)
+
+    @simple_layout('layouts/overlapping-repos.yaml')
+    def test_flat_collision(self):
+        merger = self._getMerger(scheme=zuul.model.SCHEME_FLAT)
+        repo = merger.getRepo('gerrit', 'component')
+        self.assertIsNotNone(repo)
+        repo = merger.getRepo('gerrit', 'component/component')
+        self.assertIsNone(repo)
+
+
+class TestOverlappingRepos(ZuulTestCase):
+
+    @simple_layout('layouts/overlapping-repos.yaml')
+    def test_overlapping_repos(self):
+        self.executor_server.keep_jobdir = True
+        A = self.fake_gerrit.addFakeChange('component', 'master', 'A')
+
+        self.fake_gerrit.addEvent(A.getPatchsetCreatedEvent(1))
+        self.waitUntilSettled()
+        self.assertHistory([
+            dict(name='test-job', result='SUCCESS', changes='1,1')],
+            ordered=False)
+
+        build = self.getJobFromHistory('test-job')
+        jobdir_git_dir = os.path.join(build.jobdir.src_root,
+                                      'component', '.git')
+        self.assertTrue(os.path.exists(jobdir_git_dir))
+        jobdir_git_dir = os.path.join(build.jobdir.src_root,
+                                      'subcomponent', '.git')
+        self.assertTrue(os.path.exists(jobdir_git_dir))
+
+
+class TestMergerUpgrade(ZuulTestCase):
+    tenant_config_file = 'config/single-tenant/main.yaml'
+
+    def test_merger_upgrade(self):
+        work_root = os.path.join(self.test_root, 'workspace')
+
+        # Simulate existing repos
+        org_project = os.path.join(work_root, 'review.example.com', 'org',
+                                   'project', '.git')
+        os.makedirs(org_project)
+        scheme_file = os.path.join(work_root, '.zuul_merger_scheme')
+
+        # Verify that an executor merger doesn't "upgrade" or write a
+        # scheme file.
+        self.executor_server._getMerger(
+            work_root, cache_root=None, scheme=zuul.model.SCHEME_FLAT)
+        self.assertTrue(os.path.exists(org_project))
+        self.assertFalse(os.path.exists(scheme_file))
+
+        # Verify that a "real" merger does upgrade.
+        self.executor_server._getMerger(
+            work_root, cache_root=None,
+            execution_context=False)
+
+        self.assertFalse(os.path.exists(org_project))
+        self.assertTrue(os.path.exists(scheme_file))
+        with open(scheme_file) as f:
+            self.assertEqual(f.read().strip(), 'unique')
+
+        # Verify that the next time it starts, we don't upgrade again.
+        flag_dir = os.path.join(work_root, 'flag')
+        os.makedirs(flag_dir)
+        self.executor_server._getMerger(
+            work_root, cache_root=None,
+            execution_context=False)
+
+        self.assertFalse(os.path.exists(org_project))
+        self.assertTrue(os.path.exists(scheme_file))
+        self.assertTrue(os.path.exists(flag_dir))
diff --git a/tests/unit/test_openstack.py b/tests/unit/test_openstack.py
index c5e18d8131..6b6a652b6a 100644
--- a/tests/unit/test_openstack.py
+++ b/tests/unit/test_openstack.py
@@ -68,7 +68,8 @@ class TestOpenStack(AnsibleZuulTestCase):
         # Check that a change to nova triggered a keystone clone
         executor_git_dir = os.path.join(self.executor_src_root,
                                         'review.example.com',
-                                        'openstack', 'keystone', '.git')
+                                        'openstack', 'openstack%2Fkeystone',
+                                        '.git')
         self.assertTrue(os.path.exists(executor_git_dir),
                         msg='openstack/keystone should be cloned.')
 
@@ -91,7 +92,8 @@ class TestOpenStack(AnsibleZuulTestCase):
         # Check that a change to keystone triggered a nova clone
         executor_git_dir = os.path.join(self.executor_src_root,
                                         'review.example.com',
-                                        'openstack', 'nova', '.git')
+                                        'openstack', 'openstack%2Fnova',
+                                        '.git')
         self.assertTrue(os.path.exists(executor_git_dir),
                         msg='openstack/nova should be cloned.')
 
diff --git a/tests/unit/test_web.py b/tests/unit/test_web.py
index fcee9ca0c5..516070f8f1 100644
--- a/tests/unit/test_web.py
+++ b/tests/unit/test_web.py
@@ -374,7 +374,8 @@ class TestWeb(BaseTestWeb):
                 'group_variables': {},
                 'host_variables': {},
                 'variant_description': '',
-                'voting': True
+                'voting': True,
+                'workspace_scheme': 'golang'
             }, {
                 'name': 'project-test1',
                 'abstract': False,
@@ -419,7 +420,8 @@ class TestWeb(BaseTestWeb):
                 'group_variables': {},
                 'host_variables': {},
                 'variant_description': 'stable',
-                'voting': True
+                'voting': True,
+                'workspace_scheme': 'golang'
             }], data)
 
         data = self.get_url('api/tenant/tenant-one/job/test-job').json()
@@ -462,7 +464,8 @@ class TestWeb(BaseTestWeb):
                 'group_variables': {},
                 'host_variables': {},
                 'variant_description': '',
-                'voting': True
+                'voting': True,
+                'workspace_scheme': 'golang'
             }], data)
 
     def test_find_job_complete_playbooks(self):
@@ -584,7 +587,8 @@ class TestWeb(BaseTestWeb):
                   'group_variables': {},
                   'host_variables': {},
                   'variant_description': '',
-                  'voting': True}],
+                  'voting': True,
+                  'workspace_scheme': 'golang'}],
                 [{'abstract': False,
                   'ansible_version': None,
                   'attempts': 3,
@@ -622,7 +626,8 @@ class TestWeb(BaseTestWeb):
                   'group_variables': {},
                   'host_variables': {},
                   'variant_description': '',
-                  'voting': True}],
+                  'voting': True,
+                  'workspace_scheme': 'golang'}],
                 [{'abstract': False,
                   'ansible_version': None,
                   'attempts': 3,
@@ -660,7 +665,8 @@ class TestWeb(BaseTestWeb):
                   'group_variables': {},
                   'host_variables': {},
                   'variant_description': '',
-                  'voting': True}],
+                  'voting': True,
+                  'workspace_scheme': 'golang'}],
                 [{'abstract': False,
                   'ansible_version': None,
                   'attempts': 3,
@@ -698,7 +704,8 @@ class TestWeb(BaseTestWeb):
                   'group_variables': {},
                   'host_variables': {},
                   'variant_description': '',
-                  'voting': True}]]
+                  'voting': True,
+                  'workspace_scheme': 'golang'}]]
 
         self.assertEqual(
             {
@@ -756,7 +763,8 @@ class TestWeb(BaseTestWeb):
                              'group_variables': {},
                              'host_variables': {},
                              'variant_description': '',
-                             'voting': True}
+                             'voting': True,
+                             'workspace_scheme': 'golang'}
                         ]],
                     }
                     ]
@@ -1075,6 +1083,7 @@ class TestWeb(BaseTestWeb):
                 'child_jobs': [],
                 'event_id': None,
             },
+            'workspace_scheme': 'golang',
         }
 
         self.assertEqual(job_params, resp.json())
diff --git a/zuul/configloader.py b/zuul/configloader.py
index 2f6e5628ee..43ba7d22d4 100644
--- a/zuul/configloader.py
+++ b/zuul/configloader.py
@@ -650,6 +650,7 @@ class JobParser(object):
                       'variant-description': str,
                       'post-review': bool,
                       'match-on-config-updates': bool,
+                      'workspace-scheme': vs.Any('golang', 'flat'),
     }
 
     job_name = {vs.Required('name'): str}
@@ -676,6 +677,7 @@ class JobParser(object):
         'override-branch',
         'override-checkout',
         'match-on-config-updates',
+        'workspace-scheme',
     ]
 
     def __init__(self, pcontext):
diff --git a/zuul/executor/common.py b/zuul/executor/common.py
index e81ccd19e6..d80a8f6455 100644
--- a/zuul/executor/common.py
+++ b/zuul/executor/common.py
@@ -14,6 +14,8 @@
 
 import os
 
+from zuul.lib import strings
+
 
 def construct_gearman_params(uuid, sched, nodeset, job, item, pipeline,
                              dependent_changes=[], merger_items=[],
@@ -32,7 +34,11 @@ def construct_gearman_params(uuid, sched, nodeset, job, item, pipeline,
         short_name=item.change.project.name.split('/')[-1],
         canonical_hostname=item.change.project.canonical_hostname,
         canonical_name=item.change.project.canonical_name,
-        src_dir=os.path.join('src', item.change.project.canonical_name),
+        src_dir=os.path.join('src',
+                             strings.workspace_project_path(
+                                 item.change.project.canonical_hostname,
+                                 item.change.project.name,
+                                 job.workspace_scheme)),
     )
 
     zuul_params = dict(
@@ -90,6 +96,7 @@ def construct_gearman_params(uuid, sched, nodeset, job, item, pipeline,
     params['override_checkout'] = job.override_checkout
     params['repo_state'] = item.current_build_set.repo_state
     params['ansible_version'] = job.ansible_version
+    params['workspace_scheme'] = job.workspace_scheme
 
     def make_playbook(playbook):
         d = playbook.toDict(redact_secrets=redact_secrets_and_keys)
@@ -187,7 +194,11 @@ def construct_gearman_params(uuid, sched, nodeset, job, item, pipeline,
             # project.values() is easier for callers
             canonical_name=p.canonical_name,
             canonical_hostname=p.canonical_hostname,
-            src_dir=os.path.join('src', p.canonical_name),
+            src_dir=os.path.join('src',
+                                 strings.workspace_project_path(
+                                     p.canonical_hostname,
+                                     p.name,
+                                     job.workspace_scheme)),
             required=(p in required_projects),
         ))
 
diff --git a/zuul/executor/server.py b/zuul/executor/server.py
index e7ade8f05f..dbb77069f4 100644
--- a/zuul/executor/server.py
+++ b/zuul/executor/server.py
@@ -60,6 +60,7 @@ from zuul.merger.server import BaseMergeServer, RepoLocks
 from zuul.model import (
     BuildCompletedEvent, BuildPausedEvent, BuildStartedEvent, BuildStatusEvent
 )
+import zuul.model
 from zuul.zk.event_queues import PipelineResultEventQueue
 
 BUFFER_LINES_FOR_SYNTAX = 200
@@ -823,6 +824,10 @@ class AnsibleJob(object):
         self.zuul_event_id = self.arguments.get('zuul_event_id')
         # Record ansible version being used for the cleanup phase
         self.ansible_version = self.arguments.get('ansible_version')
+        # TODO(corvus): Remove default setting after 4.3.0; this is to handle
+        # scheduler/executor version skew.
+        self.scheme = self.arguments.get('workspace_scheme',
+                                         zuul.model.SCHEME_GOLANG)
         self.log = get_annotated_logger(
             logger, self.zuul_event_id, build=job.unique)
         self.executor_server = executor_server
@@ -1083,7 +1088,8 @@ class AnsibleJob(object):
         merger = self.executor_server._getMerger(
             self.jobdir.src_root,
             self.executor_server.merge_root,
-            self.log)
+            logger=self.log,
+            scheme=self.scheme)
         repos = {}
         for project in args['projects']:
             self.log.debug("Cloning %s/%s" % (project['connection'],
@@ -1776,10 +1782,15 @@ class AnsibleJob(object):
                                                  branch)
             self.log.debug("Cloning %s@%s into new trusted space %s",
                            project, branch, root)
+            # We always use the golang scheme for playbook checkouts
+            # (so that the path indicates the canonical repo name for
+            # easy debugging; there are no concerns with collisions
+            # since we only have one repo in the working dir).
             merger = self.executor_server._getMerger(
                 root,
                 self.executor_server.merge_root,
-                self.log)
+                logger=self.log,
+                scheme=zuul.model.SCHEME_GOLANG)
             merger.checkoutBranch(
                 project.connection_name, project.name,
                 branch,
@@ -1804,6 +1815,11 @@ class AnsibleJob(object):
             # If the project is in the dependency chain, clone from
             # there so we pick up any speculative changes, otherwise,
             # clone from the cache.
+            #
+            # We always use the golang scheme for playbook checkouts
+            # (so that the path indicates the canonical repo name for
+            # easy debugging; there are no concerns with collisions
+            # since we only have one repo in the working dir).
             merger = None
             for p in args['projects']:
                 if (p['connection'] == project.connection_name and
@@ -1813,7 +1829,9 @@ class AnsibleJob(object):
                     merger = self.executor_server._getMerger(
                         root,
                         self.jobdir.src_root,
-                        self.log)
+                        logger=self.log,
+                        scheme=zuul.model.SCHEME_GOLANG,
+                        cache_scheme=self.scheme)
                     break
 
             repo_state = None
@@ -1821,7 +1839,8 @@ class AnsibleJob(object):
                 merger = self.executor_server._getMerger(
                     root,
                     self.executor_server.merge_root,
-                    self.log)
+                    logger=self.log,
+                    scheme=zuul.model.SCHEME_GOLANG)
 
                 # If we don't have this repo yet prepared we need to restore
                 # the repo state. Otherwise we have speculative merges in the
diff --git a/zuul/lib/strings.py b/zuul/lib/strings.py
index aa3dc22a52..d834aa4ef2 100644
--- a/zuul/lib/strings.py
+++ b/zuul/lib/strings.py
@@ -12,8 +12,11 @@
 # License for the specific language governing permissions and limitations
 # under the License.
 
+import os.path
 from urllib.parse import quote_plus
 
+import zuul.model
+
 
 def unique_project_name(project_name):
     parts = project_name.split('/')
@@ -21,3 +24,15 @@ def unique_project_name(project_name):
 
     name = quote_plus(project_name)
     return f'{prefix}/{name}'
+
+
+def workspace_project_path(hostname, project_name, scheme):
+    """Return the project path based on the specified scheme"""
+    if scheme == zuul.model.SCHEME_UNIQUE:
+        project_name = unique_project_name(project_name)
+        return os.path.join(hostname, project_name)
+    elif scheme == zuul.model.SCHEME_GOLANG:
+        return os.path.join(hostname, project_name)
+    elif scheme == zuul.model.SCHEME_FLAT:
+        parts = project_name.split('/')
+        return os.path.join(parts[-1])
diff --git a/zuul/merger/merger.py b/zuul/merger/merger.py
index 73dd4e86c8..7db0840ac9 100644
--- a/zuul/merger/merger.py
+++ b/zuul/merger/merger.py
@@ -28,6 +28,7 @@ import git
 import gitdb
 import paramiko
 from zuul.zk import ZooKeeperClient
+from zuul.lib import strings
 
 import zuul.model
 
@@ -723,7 +724,36 @@ class Repo(object):
         return branches
 
 
+class MergerTree:
+    """
+    A tree structure for quickly determining if a repo collides with
+    another in the same merger workspace.
+
+    Each node is a dictionary represents a path element.  The keys are
+    child path elements and their values are either another dictionary
+    for another node, or None if the child node is a git repo.
+    """
+
+    def __init__(self):
+        self.root = {}
+
+    def add(self, path):
+        parts = path.split('/')
+        root = self.root
+        for i, part in enumerate(parts[:-1]):
+            root = root.setdefault(part, {})
+            if root is None:
+                other = '/'.join(parts[:i])
+                raise Exception(f"Repo {path} collides with {other}")
+        last = parts[-1]
+        if last in root:
+            raise Exception(f"Repo {path} collides with "
+                            "an existing repo with a longer path")
+        root[last] = None
+
+
 class Merger(object):
+
     def __init__(
         self,
         working_root: str,
@@ -737,6 +767,8 @@ class Merger(object):
         logger: Optional[Logger] = None,
         execution_context: bool = False,
         git_timeout: int = 300,
+        scheme: str = None,
+        cache_scheme: str = None,
     ):
         self.logger = logger
         if logger is None:
@@ -754,20 +786,55 @@ class Merger(object):
         self.speed_time = speed_time
         self.git_timeout = git_timeout
         self.cache_root = cache_root
+        self.scheme = scheme or zuul.model.SCHEME_UNIQUE
+        self.cache_scheme = cache_scheme or zuul.model.SCHEME_UNIQUE
         # Flag to determine if the merger is used for preparing repositories
         # for job execution. This flag can be used to enable executor specific
         # behavior e.g. to keep the 'origin' remote intact.
         self.execution_context = execution_context
+        # A tree of repos in our working root for detecting collisions
+        self.repo_roots = MergerTree()
+        # If we're not in an execution context, then check to see if
+        # our working root needs a "schema" upgrade.
+        if not execution_context:
+            self._upgradeRootScheme()
+
+    def _upgradeRootScheme(self):
+        # If the scheme for the root directory has changed, delete all
+        # the repos so they can be re-cloned.
+        try:
+            with open(os.path.join(self.working_root,
+                                   '.zuul_merger_scheme')) as f:
+                scheme = f.read().strip()
+        except FileNotFoundError:
+            # The previous default was golang
+            scheme = zuul.model.SCHEME_GOLANG
+        if scheme == self.scheme:
+            return
+        if os.listdir(self.working_root):
+            self.log.info(f"Existing merger scheme {scheme} does not match "
+                          f"requested scheme {self.scheme}, deleting merger "
+                          "root (repositories will be re-cloned).")
+            shutil.rmtree(self.working_root)
+            os.makedirs(self.working_root)
+        with open(os.path.join(self.working_root,
+                               '.zuul_merger_scheme'), 'w') as f:
+            f.write(self.scheme)
 
     def _addProject(self, hostname, connection_name, project_name, url, sshkey,
                     zuul_event_id, process_worker=None):
         repo = None
         key = '/'.join([hostname, project_name])
         try:
-            path = os.path.join(self.working_root, hostname, project_name)
+            path = os.path.join(self.working_root,
+                                strings.workspace_project_path(
+                                    hostname, project_name, self.scheme))
+            self.repo_roots.add(path)
             if self.cache_root:
-                cache_path = os.path.join(self.cache_root, hostname,
-                                          project_name)
+                cache_path = os.path.join(
+                    self.cache_root,
+                    strings.workspace_project_path(
+                        hostname, project_name, self.cache_scheme))
             else:
                 cache_path = None
             repo = Repo(
diff --git a/zuul/merger/server.py b/zuul/merger/server.py
index fde1c381b9..fbf38f5702 100644
--- a/zuul/merger/server.py
+++ b/zuul/merger/server.py
@@ -104,7 +104,8 @@ class BaseMergeServer(metaclass=ABCMeta):
             self.merger_jobs)
 
     def _getMerger(self, root, cache_root, logger=None,
-                   execution_context=True):
+                   execution_context=True, scheme=None,
+                   cache_scheme=None):
         return merger.Merger(
             root,
             self.connections,
@@ -117,6 +118,8 @@ class BaseMergeServer(metaclass=ABCMeta):
             logger,
             execution_context=execution_context,
             git_timeout=self.git_timeout,
+            scheme=scheme,
+            cache_scheme=cache_scheme,
         )
 
     def _repoLock(self, connection_name, project_name):
diff --git a/zuul/model.py b/zuul/model.py
index a8c7aee26e..27815971fd 100644
--- a/zuul/model.py
+++ b/zuul/model.py
@@ -92,6 +92,11 @@ NODE_STATES = set([STATE_BUILDING,
                    STATE_HOLD,
                    STATE_DELETING])
 
+# Workspace scheme
+SCHEME_GOLANG = 'golang'
+SCHEME_FLAT = 'flat'
+SCHEME_UNIQUE = 'unique'  # Internal use only
+
 
 class ConfigurationErrorKey(object):
     """A class which attempts to uniquely identify configuration errors
@@ -1242,6 +1247,7 @@ class Job(ConfigObject):
             override_branch=None,
             override_checkout=None,
             post_review=None,
+            workspace_scheme=SCHEME_GOLANG,
         )
 
         # These are generally internal attributes which are not
@@ -1340,6 +1346,7 @@ class Job(ConfigObject):
             d['ansible_version'] = self.ansible_version
         else:
             d['ansible_version'] = None
+        d['workspace_scheme'] = self.workspace_scheme
         return d
 
     def __ne__(self, other):