diff --git a/.github/workflows/bootstrap.yaml b/.github/workflows/merge_repository.yaml
similarity index 89%
rename from .github/workflows/bootstrap.yaml
rename to .github/workflows/merge_repository.yaml
index fb30f0f681da..b3b49330a876 100644
--- a/.github/workflows/bootstrap.yaml
+++ b/.github/workflows/merge_repository.yaml
@@ -1,4 +1,4 @@
-name: Bootstrap
+name: Merge Repository
 on:
   schedule:
     - cron: '0 1 * * *' # nightly at 1 am UTC
@@ -19,19 +19,19 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - name: Generate
-        run: ./generation/bootstrap.sh
+        run: ./generation/merge_repository.sh
         env:
           USERNAME: ${{ github.actor }}
       - name: Compile
-        working-directory: generation/monorepo/google-cloud-java
+        working-directory: generation/monorepo/google-cloud-java-merged
         run: mvn compile -T C1 -B
       - name: Unit Tests
-        working-directory: generation/monorepo/google-cloud-java
+        working-directory: generation/monorepo/google-cloud-java-merged
         run: mvn test -T C1 -B
       - name: Push monorepo to branch
         if: ${{ github.event_name != 'pull_request' }}
         run: |
-          cd generation/monorepo/google-cloud-java
+          cd generation/monorepo/google-cloud-java-merged
           git remote add monorepo https://${{ github.actor }}:${{ github.token }}@github.com/${{ github.repository }}.git
           git push -f monorepo main:bootstrap_output
       - name: Push diff to branch
diff --git a/generation/README.md b/generation/README.md
index e75b73a3322e..b3c2056fbfcb 100644
--- a/generation/README.md
+++ b/generation/README.md
@@ -3,13 +3,14 @@
 ## Using scripts independently
 
 Most of the scripts in this directory can be used independently to do file updates across all modules.
-They are also used and tested by `bootstrap.sh`.
+They are also used and tested by `merge_repository.sh`.
 
-## Generating the monorepo
+## Merge repository into the monorepo
 
-Built by running [bootstrap.sh](bootstrap.sh).
+Built by running [merge_repository.sh](merge_repository.sh).
 
-The script creates a new Git repository in `monorepo/google-cloud-java`.
+The script creates a new Git repository in `monorepo/google-cloud-java` by merging
+the repositories in the input.
 After running the script locally, you can `cd` into the generated repository and build the project.
 
 ```shell
diff --git a/generation/bootstrap.sh b/generation/merge_repository.sh
similarity index 85%
rename from generation/bootstrap.sh
rename to generation/merge_repository.sh
index 5fe140bb8a41..f1bb06a9f93d 100755
--- a/generation/bootstrap.sh
+++ b/generation/merge_repository.sh
@@ -12,7 +12,7 @@ cd "$(dirname "$0")"
 rm -rf monorepo
 mkdir monorepo
 
-cp bootstrap.sh monorepo
+cp merge_repository.sh monorepo
 cp repos.txt monorepo
 
 cd monorepo
@@ -20,10 +20,10 @@ cd monorepo
 git clone https://github.com/newren/git-filter-repo.git
 export PATH=$PATH:`pwd`/git-filter-repo
 
-mkdir google-cloud-java
+merged_repository=google-cloud-java-merged
+git clone https://github.com/googleapis/google-cloud-java "${merged_repository}"
 
-cd google-cloud-java
-git init -b main
+cd "${merged_repository}"
 
 cat ../repos.txt | while read service
 do
@@ -51,7 +51,7 @@ do
   git config --add secrets.allowed "dest.*src"
   git commit -am "chore: setup owlbot configuration"
 
-  cd ../google-cloud-java
+  cd "../${merged_repository}"
   git remote add ${service} ../${service}
   git config --add secrets.allowed "dest.*src"
   git fetch ${service} #--tags
@@ -60,7 +60,7 @@ do
   rm -rf ../${service}
 done
 
-# cwd: monorepo/google-cloud-java
+# cwd: monorepo/google-cloud-java-merged
 echo "Working directory: $(pwd)"
 
 cp -R ../../../google-cloud-jar-parent google-cloud-jar-parent
@@ -72,18 +72,20 @@ git commit -m 'chore: add template files'
 ../../generate_root_pom.sh
 
 git add pom.xml
-git commit -am 'chore: create aggregator pom'
+git commit -am 'chore: create aggregator pom' --allow-empty
 
 # Point modules poms and BOMs to the aggregator pom as parent
 bash ../../set_parent_pom.sh
 
 git add --all
-git commit -am 'chore: point modules to the aggregator pom as parent'
+git commit -am 'chore: point modules to the aggregator pom as parent' \
+    --allow-empty
 
 ../../consolidate_config.sh
 
 git add --all
-git commit -am 'chore: consolidate config to parent'
+git commit -am 'chore: consolidate config to parent' \
+    --allow-empty
 
 ../../generate_gapic_bom.sh
 
@@ -91,33 +93,37 @@ git commit -am 'chore: consolidate config to parent'
 ../../generate_root_pom.sh
 
 git add gapic-libraries-bom/pom.xml
-git commit -am 'chore: create gapic-libraries-bom'
+git commit -am 'chore: create gapic-libraries-bom' \
+    --allow-empty
 
 cp ../../gapic_bom_versions.txt gapic-libraries-bom/versions.txt
 
 ../../delete_non_generated_samples.sh
 
 git add --all
-git commit -am 'chore: delete non-auto-generated samples'
+git commit -am 'chore: delete non-auto-generated samples' \
+    --allow-empty
 
 ../../generate_root_versions_txt.sh
 ../../update_versions.sh -s
 ../../apply_current_versions.sh
 
 git add --all
-git commit -am 'chore: update versions to latest in maven'
+git commit -am 'chore: update versions to latest in maven' \
+    --allow-empty
 
 ../../update_owlbot_postprocessor_config.sh
 
 git add --all
-git commit -am 'chore: remove and disable owlbot postprocessor templates'
+git commit -am 'chore: remove and disable owlbot postprocessor templates' \
+    --allow-empty
 
 for F in `find . -maxdepth 2 -name '.OwlBot.yaml'`; do sh ../../set_owlbot_config.sh $F; done
 git commit -am 'chore: set owlbot copy config' --allow-empty
 
 # create a monorepo/diff repo
 cd ..
-cp -R google-cloud-java split
+cp -R "${merged_repository}" split
 rm -rf split/.git
 git clone -b main --single-branch https://github.com/googleapis/google-cloud-java.git shadow
 cp -R shadow/.git split/.git
diff --git a/generation/repos.txt b/generation/repos.txt
index 99ca132909ae..58c8f1201c44 100644
--- a/generation/repos.txt
+++ b/generation/repos.txt
@@ -1,132 +1 @@
-java-accessapproval
-java-accesscontextmanager
-java-aiplatform
-java-analytics-admin
-java-analytics-data
-java-api-gateway
-java-apigee-connect
-java-apigee-registry
-java-apikeys
-java-appengine-admin
-java-area120-tables
-java-artifact-registry
-java-asset
-java-assured-workloads
-java-automl
-java-bare-metal-solution
-java-batch
-java-beyondcorp-appconnections
-java-beyondcorp-appconnectors
-java-beyondcorp-appgateways
-java-beyondcorp-clientconnectorservices
-java-beyondcorp-clientgateways
-java-bigquery-data-exchange
-java-bigqueryconnection
-java-bigquerydatatransfer
-java-bigquerymigration
-java-bigqueryreservation
-java-billing
-java-billingbudgets
-java-binary-authorization
-java-certificate-manager
-java-channel
-java-cloudbuild
-java-cloudcommerceconsumerprocurement
-java-compute
-java-contact-center-insights
-java-container
-java-containeranalysis
-java-data-fusion
-java-datacatalog
-java-dataflow
-java-dataform
-java-datalabeling
-java-dataplex
-java-dataproc
-java-dataproc-metastore
-java-datastream
-java-debugger-client
-java-deploy
-java-dialogflow
-java-dialogflow-cx
-java-dlp
-java-dms
-java-dns
-java-document-ai
-java-domains
-java-errorreporting
-java-essential-contacts
-java-eventarc
-java-eventarc-publishing
-java-filestore
-java-functions
-java-game-servers
-java-gke-backup
-java-gke-connect-gateway
-java-gke-multi-cloud
-java-gkehub
-java-grafeas
-java-gsuite-addons
-java-iam-admin
-java-iamcredentials
-java-ids
-java-iot
-java-kms
-java-language
-java-life-sciences
-java-managed-identities
-java-mediatranslation
-java-memcache
-java-monitoring
-java-monitoring-dashboards
-java-network-management
-java-network-security
-java-networkconnectivity
-java-notebooks
-java-notification
-java-optimization
-java-orchestration-airflow
-java-orgpolicy
-java-os-config
-java-os-login
-java-phishingprotection
-java-policy-troubleshooter
-java-private-catalog
-java-profiler
-java-recaptchaenterprise
-java-recommendations-ai
-java-recommender
-java-redis
-java-resource-settings
-java-resourcemanager
-java-retail
-java-run
-java-scheduler
-java-secretmanager
-java-security-private-ca
-java-securitycenter
-java-securitycenter-settings
-java-service-control
-java-service-management
-java-service-usage
-java-servicedirectory
-java-shell
-java-speech
-java-storage-transfer
-java-talent
-java-tasks
-java-texttospeech
-java-tpu
-java-trace
-java-translate
-java-video-intelligence
-java-video-live-stream
-java-video-stitcher
-java-video-transcoder
-java-vision
-java-vmmigration
-java-vpcaccess
-java-webrisk
-java-websecurityscanner
-java-workflow-executions
-java-workflows
+java-logging
\ No newline at end of file