diff --git a/tests/fixtures/config/merge-modes/git/common-config/zuul.yaml b/tests/fixtures/config/merges/git/common-config/zuul.yaml
similarity index 78%
rename from tests/fixtures/config/merge-modes/git/common-config/zuul.yaml
rename to tests/fixtures/config/merges/git/common-config/zuul.yaml
index a7a4c78..bb91f3a 100644
--- a/tests/fixtures/config/merge-modes/git/common-config/zuul.yaml
+++ b/tests/fixtures/config/merges/git/common-config/zuul.yaml
@@ -40,6 +40,15 @@
     name:
       project-test1
 
+- job:
+    name:
+      project-test2
+
+- job:
+    name:
+      project-merge
+    hold-following-changes: true
+
 - project:
     name: org/project-merge
     merge-mode: merge
@@ -60,3 +69,12 @@
     gate:
       jobs:
         - project-test1
+
+- project:
+    name: org/project-merge-branches
+    merge-mode: cherry-pick
+    gate:
+      jobs:
+        - project-merge:
+            jobs:
+              - project-test1
diff --git a/tests/fixtures/config/merge-modes/git/org_project-cherry-pick/README b/tests/fixtures/config/merges/git/org_project-cherry-pick/README
similarity index 100%
rename from tests/fixtures/config/merge-modes/git/org_project-cherry-pick/README
rename to tests/fixtures/config/merges/git/org_project-cherry-pick/README
diff --git a/tests/fixtures/config/merge-modes/git/org_project-cherry-pick/README b/tests/fixtures/config/merges/git/org_project-merge-branches/README
similarity index 100%
copy from tests/fixtures/config/merge-modes/git/org_project-cherry-pick/README
copy to tests/fixtures/config/merges/git/org_project-merge-branches/README
diff --git a/tests/fixtures/config/merge-modes/git/org_project-merge-resolve/README b/tests/fixtures/config/merges/git/org_project-merge-resolve/README
similarity index 100%
rename from tests/fixtures/config/merge-modes/git/org_project-merge-resolve/README
rename to tests/fixtures/config/merges/git/org_project-merge-resolve/README
diff --git a/tests/fixtures/config/merge-modes/git/org_project-merge/README b/tests/fixtures/config/merges/git/org_project-merge/README
similarity index 100%
rename from tests/fixtures/config/merge-modes/git/org_project-merge/README
rename to tests/fixtures/config/merges/git/org_project-merge/README
diff --git a/tests/fixtures/config/merge-modes/main.yaml b/tests/fixtures/config/merges/main.yaml
similarity index 100%
rename from tests/fixtures/config/merge-modes/main.yaml
rename to tests/fixtures/config/merges/main.yaml
diff --git a/tests/unit/test_scheduler.py b/tests/unit/test_scheduler.py
index 17e0cdb..ee34d56 100755
--- a/tests/unit/test_scheduler.py
+++ b/tests/unit/test_scheduler.py
@@ -1041,41 +1041,6 @@
         self.assertIn('project-post', job_names)
 
     @skip("Disabled for early v3 development")
-    def test_build_configuration_branch(self):
-        "Test that the right commits are on alternate branches"
-
-        self.gearman_server.hold_jobs_in_queue = True
-        A = self.fake_gerrit.addFakeChange('org/project', 'mp', 'A')
-        B = self.fake_gerrit.addFakeChange('org/project', 'mp', 'B')
-        C = self.fake_gerrit.addFakeChange('org/project', 'mp', 'C')
-        A.addApproval('code-review', 2)
-        B.addApproval('code-review', 2)
-        C.addApproval('code-review', 2)
-        self.fake_gerrit.addEvent(A.addApproval('approved', 1))
-        self.fake_gerrit.addEvent(B.addApproval('approved', 1))
-        self.fake_gerrit.addEvent(C.addApproval('approved', 1))
-        self.waitUntilSettled()
-
-        self.gearman_server.release('.*-merge')
-        self.waitUntilSettled()
-        self.gearman_server.release('.*-merge')
-        self.waitUntilSettled()
-        self.gearman_server.release('.*-merge')
-        self.waitUntilSettled()
-        queue = self.gearman_server.getQueue()
-        ref = self.getParameter(queue[-1], 'ZUUL_REF')
-        self.gearman_server.hold_jobs_in_queue = False
-        self.gearman_server.release()
-        self.waitUntilSettled()
-
-        path = os.path.join(self.git_root, "org/project")
-        repo = git.Repo(path)
-        repo_messages = [c.message.strip() for c in repo.iter_commits(ref)]
-        repo_messages.reverse()
-        correct_messages = ['initial commit', 'mp commit', 'A-1', 'B-1', 'C-1']
-        self.assertEqual(repo_messages, correct_messages)
-
-    @skip("Disabled for early v3 development")
     def test_build_configuration_branch_interaction(self):
         "Test that switching between branches works"
         self.test_build_configuration()
@@ -1086,89 +1051,6 @@
         repo.heads.master.commit = repo.commit('init')
         self.test_build_configuration()
 
-    @skip("Disabled for early v3 development")
-    def test_build_configuration_multi_branch(self):
-        "Test that dependent changes on multiple branches are merged"
-
-        self.gearman_server.hold_jobs_in_queue = True
-        A = self.fake_gerrit.addFakeChange('org/project', 'master', 'A')
-        B = self.fake_gerrit.addFakeChange('org/project', 'mp', 'B')
-        C = self.fake_gerrit.addFakeChange('org/project', 'master', 'C')
-        A.addApproval('code-review', 2)
-        B.addApproval('code-review', 2)
-        C.addApproval('code-review', 2)
-        self.fake_gerrit.addEvent(A.addApproval('approved', 1))
-        self.fake_gerrit.addEvent(B.addApproval('approved', 1))
-        self.fake_gerrit.addEvent(C.addApproval('approved', 1))
-        self.waitUntilSettled()
-        queue = self.gearman_server.getQueue()
-        job_A = None
-        for job in queue:
-            if 'project-merge' in job.name:
-                job_A = job
-        ref_A = self.getParameter(job_A, 'ZUUL_REF')
-        commit_A = self.getParameter(job_A, 'ZUUL_COMMIT')
-        self.log.debug("Got Zuul ref for change A: %s" % ref_A)
-        self.log.debug("Got Zuul commit for change A: %s" % commit_A)
-
-        self.gearman_server.release('.*-merge')
-        self.waitUntilSettled()
-        queue = self.gearman_server.getQueue()
-        job_B = None
-        for job in queue:
-            if 'project-merge' in job.name:
-                job_B = job
-        ref_B = self.getParameter(job_B, 'ZUUL_REF')
-        commit_B = self.getParameter(job_B, 'ZUUL_COMMIT')
-        self.log.debug("Got Zuul ref for change B: %s" % ref_B)
-        self.log.debug("Got Zuul commit for change B: %s" % commit_B)
-
-        self.gearman_server.release('.*-merge')
-        self.waitUntilSettled()
-        queue = self.gearman_server.getQueue()
-        for job in queue:
-            if 'project-merge' in job.name:
-                job_C = job
-        ref_C = self.getParameter(job_C, 'ZUUL_REF')
-        commit_C = self.getParameter(job_C, 'ZUUL_COMMIT')
-        self.log.debug("Got Zuul ref for change C: %s" % ref_C)
-        self.log.debug("Got Zuul commit for change C: %s" % commit_C)
-        self.gearman_server.hold_jobs_in_queue = False
-        self.gearman_server.release()
-        self.waitUntilSettled()
-
-        path = os.path.join(self.git_root, "org/project")
-        repo = git.Repo(path)
-
-        repo_messages = [c.message.strip()
-                         for c in repo.iter_commits(ref_C)]
-        repo_shas = [c.hexsha for c in repo.iter_commits(ref_C)]
-        repo_messages.reverse()
-        correct_messages = ['initial commit', 'A-1', 'C-1']
-        # Ensure the right commits are in the history for this ref
-        self.assertEqual(repo_messages, correct_messages)
-        # Ensure ZUUL_REF -> ZUUL_COMMIT
-        self.assertEqual(repo_shas[0], commit_C)
-
-        repo_messages = [c.message.strip()
-                         for c in repo.iter_commits(ref_B)]
-        repo_shas = [c.hexsha for c in repo.iter_commits(ref_B)]
-        repo_messages.reverse()
-        correct_messages = ['initial commit', 'mp commit', 'B-1']
-        self.assertEqual(repo_messages, correct_messages)
-        self.assertEqual(repo_shas[0], commit_B)
-
-        repo_messages = [c.message.strip()
-                         for c in repo.iter_commits(ref_A)]
-        repo_shas = [c.hexsha for c in repo.iter_commits(ref_A)]
-        repo_messages.reverse()
-        correct_messages = ['initial commit', 'A-1']
-        self.assertEqual(repo_messages, correct_messages)
-        self.assertEqual(repo_shas[0], commit_A)
-
-        self.assertNotEqual(ref_A, ref_B, ref_C)
-        self.assertNotEqual(commit_A, commit_B, commit_C)
-
     def test_dependent_changes_dequeue(self):
         "Test that dependent patches are not needlessly tested"
 
@@ -4701,8 +4583,8 @@
             body[3])
 
 
-class TestSchedulerMergeModes(ZuulTestCase):
-    tenant_config_file = 'config/merge-modes/main.yaml'
+class TestSchedulerMerges(ZuulTestCase):
+    tenant_config_file = 'config/merges/main.yaml'
 
     def _test_project_merge_mode(self, mode):
         self.launch_server.keep_jobdir = False
@@ -4762,3 +4644,137 @@
             'C-1']
         result = self._test_project_merge_mode('cherry-pick')
         self.assertEqual(result, expected_messages)
+
+    def test_merge_branch(self):
+        "Test that the right commits are on alternate branches"
+        self.create_branch('org/project-merge-branches', 'mp')
+
+        self.launch_server.hold_jobs_in_build = True
+        A = self.fake_gerrit.addFakeChange(
+            'org/project-merge-branches', 'mp', 'A')
+        B = self.fake_gerrit.addFakeChange(
+            'org/project-merge-branches', 'mp', 'B')
+        C = self.fake_gerrit.addFakeChange(
+            'org/project-merge-branches', 'mp', 'C')
+        A.addApproval('code-review', 2)
+        B.addApproval('code-review', 2)
+        C.addApproval('code-review', 2)
+        self.fake_gerrit.addEvent(A.addApproval('approved', 1))
+        self.fake_gerrit.addEvent(B.addApproval('approved', 1))
+        self.fake_gerrit.addEvent(C.addApproval('approved', 1))
+        self.waitUntilSettled()
+
+        self.launch_server.release('.*-merge')
+        self.waitUntilSettled()
+        self.launch_server.release('.*-merge')
+        self.waitUntilSettled()
+        self.launch_server.release('.*-merge')
+        self.waitUntilSettled()
+
+        build = self.builds[-1]
+        self.assertEqual(self.getParameter(build, 'ZUUL_BRANCH'), 'mp')
+        ref = self.getParameter(build, 'ZUUL_REF')
+        path = os.path.join(
+            build.jobdir.git_root, 'org/project-merge-branches')
+        repo = git.Repo(path)
+
+        repo_messages = [c.message.strip() for c in repo.iter_commits(ref)]
+        repo_messages.reverse()
+        correct_messages = [
+            'initial commit',
+            'add content from fixture',
+            'mp commit',
+            'A-1', 'B-1', 'C-1']
+        self.assertEqual(repo_messages, correct_messages)
+
+        self.launch_server.hold_jobs_in_build = False
+        self.launch_server.release()
+        self.waitUntilSettled()
+
+    def test_merge_multi_branch(self):
+        "Test that dependent changes on multiple branches are merged"
+        self.create_branch('org/project-merge-branches', 'mp')
+
+        self.launch_server.hold_jobs_in_build = True
+        A = self.fake_gerrit.addFakeChange(
+            'org/project-merge-branches', 'master', 'A')
+        B = self.fake_gerrit.addFakeChange(
+            'org/project-merge-branches', 'mp', 'B')
+        C = self.fake_gerrit.addFakeChange(
+            'org/project-merge-branches', 'master', 'C')
+        A.addApproval('code-review', 2)
+        B.addApproval('code-review', 2)
+        C.addApproval('code-review', 2)
+        self.fake_gerrit.addEvent(A.addApproval('approved', 1))
+        self.fake_gerrit.addEvent(B.addApproval('approved', 1))
+        self.fake_gerrit.addEvent(C.addApproval('approved', 1))
+        self.waitUntilSettled()
+
+        job_A = None
+        for job in self.builds:
+            if 'project-merge' in job.name:
+                job_A = job
+        ref_A = self.getParameter(job_A, 'ZUUL_REF')
+        commit_A = self.getParameter(job_A, 'ZUUL_COMMIT')
+        self.log.debug("Got Zuul ref for change A: %s" % ref_A)
+        self.log.debug("Got Zuul commit for change A: %s" % commit_A)
+
+        path = os.path.join(
+            job_A.jobdir.git_root, "org/project-merge-branches")
+        repo = git.Repo(path)
+        repo_messages = [c.message.strip()
+                         for c in repo.iter_commits(ref_A)]
+        repo_messages.reverse()
+        correct_messages = [
+            'initial commit', 'add content from fixture', 'A-1']
+        self.assertEqual(repo_messages, correct_messages)
+
+        self.launch_server.release('.*-merge')
+        self.waitUntilSettled()
+
+        job_B = None
+        for job in self.builds:
+            if 'project-merge' in job.name:
+                job_B = job
+        ref_B = self.getParameter(job_B, 'ZUUL_REF')
+        commit_B = self.getParameter(job_B, 'ZUUL_COMMIT')
+        self.log.debug("Got Zuul ref for change B: %s" % ref_B)
+        self.log.debug("Got Zuul commit for change B: %s" % commit_B)
+
+        path = os.path.join(
+            job_B.jobdir.git_root, "org/project-merge-branches")
+        repo = git.Repo(path)
+        repo_messages = [c.message.strip()
+                         for c in repo.iter_commits(ref_B)]
+        repo_messages.reverse()
+        correct_messages = [
+            'initial commit', 'add content from fixture', 'mp commit', 'B-1']
+        self.assertEqual(repo_messages, correct_messages)
+
+        self.launch_server.release('.*-merge')
+        self.waitUntilSettled()
+
+        job_C = None
+        for job in self.builds:
+            if 'project-merge' in job.name:
+                job_C = job
+        ref_C = self.getParameter(job_C, 'ZUUL_REF')
+        commit_C = self.getParameter(job_C, 'ZUUL_COMMIT')
+        self.log.debug("Got Zuul ref for change C: %s" % ref_C)
+        self.log.debug("Got Zuul commit for change C: %s" % commit_C)
+        path = os.path.join(
+            job_C.jobdir.git_root, "org/project-merge-branches")
+        repo = git.Repo(path)
+        repo_messages = [c.message.strip()
+                         for c in repo.iter_commits(ref_C)]
+
+        repo_messages.reverse()
+        correct_messages = [
+            'initial commit', 'add content from fixture',
+            'A-1', 'C-1']
+        # Ensure the right commits are in the history for this ref
+        self.assertEqual(repo_messages, correct_messages)
+
+        self.launch_server.hold_jobs_in_build = False
+        self.launch_server.release()
+        self.waitUntilSettled()
diff --git a/zuul/driver/timer/__init__.py b/zuul/driver/timer/__init__.py
index 4db779b..b8979c4 100644
--- a/zuul/driver/timer/__init__.py
+++ b/zuul/driver/timer/__init__.py
@@ -76,12 +76,12 @@
                     jobs.append(job)
 
     def _onTrigger(self, tenant, pipeline_name, timespec):
-        for project in tenant.layout.projects.values():
+        for project_name in tenant.layout.project_configs.keys():
             event = TriggerEvent()
             event.type = 'timer'
             event.timespec = timespec
             event.forced_pipeline = pipeline_name
-            event.project_name = project.name
+            event.project_name = project_name
             self.log.debug("Adding event %s" % event)
             self.sched.addEvent(event)
 
diff --git a/zuul/manager/__init__.py b/zuul/manager/__init__.py
index 7ee1040..87de645 100644
--- a/zuul/manager/__init__.py
+++ b/zuul/manager/__init__.py
@@ -67,15 +67,16 @@
         def log_jobs(tree, indent=0):
             istr = '    ' + ' ' * indent
             if tree.job:
+                # TODOv3(jeblair): represent matchers
                 efilters = ''
-                for b in tree.job._branches:
-                    efilters += str(b)
-                for f in tree.job._files:
-                    efilters += str(f)
-                if tree.job.skip_if_matcher:
-                    efilters += str(tree.job.skip_if_matcher)
-                if efilters:
-                    efilters = ' ' + efilters
+                # for b in tree.job._branches:
+                #     efilters += str(b)
+                # for f in tree.job._files:
+                #     efilters += str(f)
+                # if tree.job.skip_if_matcher:
+                #     efilters += str(tree.job.skip_if_matcher)
+                # if efilters:
+                #     efilters = ' ' + efilters
                 tags = []
                 if tree.job.hold_following_changes:
                     tags.append('[hold]')
@@ -89,10 +90,11 @@
             for x in tree.job_trees:
                 log_jobs(x, indent + 2)
 
-        for p in layout.projects.values():
-            tree = self.pipeline.getJobTree(p)
+        for project_name in layout.project_configs.keys():
+            project = self.pipeline.source.getProject(project_name)
+            tree = self.pipeline.getJobTree(project)
             if tree:
-                self.log.info("    %s" % p)
+                self.log.info("    %s" % project)
                 log_jobs(tree)
         self.log.info("  On start:")
         self.log.info("    %s" % self.pipeline.start_actions)
diff --git a/zuul/model.py b/zuul/model.py
index 2c3c7b3..00de007 100644
--- a/zuul/model.py
+++ b/zuul/model.py
@@ -1827,7 +1827,6 @@
 
     def __init__(self):
         self.tenant = None
-        self.projects = {}
         self.project_configs = {}
         self.project_templates = {}
         self.pipelines = OrderedDict()