diff --git a/prow/cluster/jobs/istio/istio.io/istio.istio.io.master.gen.yaml b/prow/cluster/jobs/istio/istio.io/istio.istio.io.master.gen.yaml
index e70788277ec..032737500ad 100644
--- a/prow/cluster/jobs/istio/istio.io/istio.istio.io.master.gen.yaml
+++ b/prow/cluster/jobs/istio/istio.io/istio.istio.io.master.gen.yaml
@@ -7,6 +7,10 @@ periodics:
   cron: 0 2 * * *
   decorate: true
   extra_refs:
+  - base_ref: master
+    org: istio
+    path_alias: istio.io/istio.io
+    repo: istio.io
   - base_ref: master
     org: istio
     path_alias: istio.io/test-infra
@@ -15,7 +19,7 @@ periodics:
   spec:
     containers:
     - command:
-      - ./tools/automator/automator.sh
+      - ../test-infra/tools/automator/automator.sh
       - --org=istio
       - --repo=istio.io
       - '--title=Automator: update istio.io@$AUTOMATOR_SRC_BRANCH reference docs'
@@ -58,6 +62,10 @@ periodics:
   cron: 0 2 * * 0
   decorate: true
   extra_refs:
+  - base_ref: master
+    org: istio
+    path_alias: istio.io/istio.io
+    repo: istio.io
   - base_ref: master
     org: istio
     path_alias: istio.io/test-infra
@@ -66,7 +74,7 @@ periodics:
   spec:
     containers:
     - command:
-      - ./tools/automator/automator.sh
+      - ../test-infra/tools/automator/automator.sh
       - --org=istio
       - --repo=istio.io
       - '--title=Automator: update istio@$AUTOMATOR_SRC_BRANCH test reference'
diff --git a/prow/config/cmd/generate.go b/prow/config/cmd/generate.go
index c0f375b91ff..96de3f50a46 100644
--- a/prow/config/cmd/generate.go
+++ b/prow/config/cmd/generate.go
@@ -62,7 +62,10 @@ func main() {
 		panic("too many arguments")
 	}
 
-	settings := config.ReadGlobalSettings(filepath.Join(*inputDir, ".global.yaml"))
+	var settings config.GlobalConfig
+	if _, err := os.Stat(filepath.Join(*inputDir, ".global.yaml")); !os.IsNotExist(err) {
+		settings = config.ReadGlobalSettings(filepath.Join(*inputDir, ".global.yaml"))
+	}
 	cli := &config.Client{GlobalConfig: settings}
 
 	if os.Args[1] == "branch" {
diff --git a/prow/config/generate.go b/prow/config/generate.go
index 37fe6115e57..1b4b5322b67 100644
--- a/prow/config/generate.go
+++ b/prow/config/generate.go
@@ -16,6 +16,7 @@ package config
 
 import (
 	"bytes"
+	"errors"
 	"fmt"
 	"io/ioutil"
 	"os"
@@ -98,6 +99,7 @@ type JobsConfig struct {
 	Repo     string   `json:"repo,omitempty"`
 	Org      string   `json:"org,omitempty"`
 	Branches []string `json:"branches,omitempty"`
+	CloneURI string   `json:"clone_uri,omitempty"`
 
 	Matrix map[string][]string `json:"matrix,omitempty"`
 
@@ -372,10 +374,9 @@ func (cli *Client) ConvertJobConfig(jobsConfig JobsConfig, branch string) config
 				}
 				name += "_periodic"
 
-				// If no repos are provided, add itself to the repo list.
-				if len(job.Repos) == 0 {
-					job.Repos = []string{jobsConfig.Org + "/" + jobsConfig.Repo}
-				}
+				// For periodic jobs, the repo needs to be added to the clonerefs and its root directory
+				// should be set as the working directory, so add itself to the repo list here.
+				job.Repos = append([]string{jobsConfig.Org + "/" + jobsConfig.Repo}, job.Repos...)
 				periodic := config.Periodic{
 					JobBase:  createJobBase(settings, jobsConfig, job, name, branch, jobsConfig.Resources),
 					Interval: job.Interval,
@@ -470,7 +471,7 @@ func (cli *Client) DiffConfig(result config.JobConfig, existing config.JobConfig
 
 // FilterReleaseBranchingJobs filters then returns jobs with release branching enabled.
 func FilterReleaseBranchingJobs(jobs []Job) []Job {
-	jobsF := []Job{}
+	jobsF := make([]Job, 0)
 	for _, j := range jobs {
 		if j.DisableReleaseBranching {
 			continue
@@ -663,15 +664,16 @@ func createJobBase(globalConfig GlobalConfig, jobConfig JobsConfig, job Job,
 }
 
 func createExtraRefs(extraRepos []string, defaultBranch string, pathAliases map[string]string) []prowjob.Refs {
-	refs := []prowjob.Refs{}
+	refs := make([]prowjob.Refs, 0)
 	for _, extraRepo := range extraRepos {
 		branch := defaultBranch
 		repobranch := strings.Split(extraRepo, "@")
 		if len(repobranch) > 1 {
 			branch = repobranch[1]
 		}
-		orgrepo := strings.Split(repobranch[0], "/")
-		org, repo := orgrepo[0], orgrepo[1]
+		orgrepo := repobranch[0]
+		repo := orgrepo[strings.LastIndex(orgrepo, "/")+1:]
+		org := strings.TrimSuffix(orgrepo, "/"+repo)
 		ref := prowjob.Refs{
 			Org:     org,
 			Repo:    repo,
@@ -680,6 +682,10 @@ func createExtraRefs(extraRepos []string, defaultBranch string, pathAliases map[
 		if pa, ok := pathAliases[org]; ok {
 			ref.PathAlias = fmt.Sprintf("%s/%s", pa, repo)
 		}
+		// If the org name contains '/', it's not a GitHub org, so CloneURI needs to be explicitly set.
+		if strings.Contains(org, "/") {
+			ref.CloneURI = "https://" + orgrepo
+		}
 		refs = append(refs, ref)
 	}
 	return refs
@@ -741,9 +747,13 @@ func applyMatrix(yamlStr string, matrix map[string][]string) []string {
 
 	combs := make([]string, 0)
 	for _, exp := range subsExps {
-		exp = strings.TrimPrefix(exp, "matrix.")
-		if _, ok := matrix[exp]; ok {
-			combs = append(combs, exp)
+		if strings.HasPrefix(exp, "matrix.") {
+			exp = strings.TrimPrefix(exp, "matrix.")
+			if _, ok := matrix[exp]; ok {
+				combs = append(combs, exp)
+			} else {
+				exit(errors.New("dimension is not configured in the matrix"), exp)
+			}
 		}
 	}
 
diff --git a/prow/config/jobs/envoy.yaml b/prow/config/jobs/envoy.yaml
index 6eaea32b0ab..c6e54dcd5c3 100644
--- a/prow/config/jobs/envoy.yaml
+++ b/prow/config/jobs/envoy.yaml
@@ -51,7 +51,7 @@ jobs:
   - --token-path=/etc/github-token/oauth
   - --cmd=scripts/update_envoy.sh $AUTOMATOR_SHA $AUTOMATOR_SHA_COMMIT_DATE
   requirements: [github]
-  repos: [istio/envoy@master, istio/test-infra@master]
+  repos: [istio/test-infra@master]
   image: gcr.io/istio-testing/build-tools:master-2021-03-01T22-30-49
   timeout: 4h
 
diff --git a/prow/config/jobs/istio.io.yaml b/prow/config/jobs/istio.io.yaml
index 37044491e21..257dbf2ae27 100644
--- a/prow/config/jobs/istio.io.yaml
+++ b/prow/config/jobs/istio.io.yaml
@@ -53,7 +53,7 @@ jobs:
     types: [periodic]
     cron: "0 2 * * *"  # every day at 02:00AM UTC
     command:
-    - ./tools/automator/automator.sh
+    - ../test-infra/tools/automator/automator.sh
     - --org=istio
     - --repo=istio.io
     - "--title=Automator: update istio.io@$AUTOMATOR_SRC_BRANCH reference docs"
@@ -69,7 +69,7 @@ jobs:
     types: [periodic]
     cron: "0 2 * * 0"  # every Sunday at 02:00AM UTC
     command:
-    - ./tools/automator/automator.sh
+    - ../test-infra/tools/automator/automator.sh
     - --org=istio
     - --repo=istio.io
     - "--title=Automator: update istio@$AUTOMATOR_SRC_BRANCH test reference"
diff --git a/prow/config/jobs/test-infra.yaml b/prow/config/jobs/test-infra.yaml
index 47003fd33c8..e34dc305ec0 100644
--- a/prow/config/jobs/test-infra.yaml
+++ b/prow/config/jobs/test-infra.yaml
@@ -157,4 +157,3 @@ jobs:
     - --tag=v[0-9]{8}-[a-f0-9]{10}
     - --var=image
     requirements: [github]
-    repos: [istio/test-infra]
diff --git a/prow/genjobs/cmd/genjobs/main.go b/prow/genjobs/cmd/genjobs/main.go
index aa3760b5797..c938212f21b 100644
--- a/prow/genjobs/cmd/genjobs/main.go
+++ b/prow/genjobs/cmd/genjobs/main.go
@@ -827,7 +827,7 @@ func updateExtraRefs(o options, job *config.UtilityConfig) {
 		}
 	}
 	if len(o.ExtraRefs) > 0 {
-		job.ExtraRefs = o.ExtraRefs
+		job.ExtraRefs = append(job.ExtraRefs, o.ExtraRefs...)
 	}
 }