diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 5d04eb4bc4e0..9af1a5882ce2 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -112,6 +112,7 @@ jobs:
     outputs:
       packages: ${{ steps.filter.outputs.changes }}
     steps:
+    - uses: actions/checkout@v4
     - uses: dorny/paths-filter@fbd0ab8f3e69293af611ebaee6363fc25e6d187d # v4.0.1
       id: filter
       with:
@@ -338,8 +339,8 @@ jobs:
     - run: .kokoro/build.sh
       env:
         JOB_TYPE: lint
-        HEAD_SHA: ${{ github.event.pull_request.head.sha }}
-        BASE_SHA: ${{ github.event.pull_request.base.sha }}
+        HEAD_SHA: ${{ github.event.pull_request.head.sha || github.sha }}
+        BASE_SHA: ${{ github.event.pull_request.base.sha || github.event.before }}
   enforcer:
     runs-on: ubuntu-latest
     steps:
diff --git a/.github/workflows/java-bigtable-ci.yaml b/.github/workflows/java-bigtable-ci.yaml
index ef6db6e93a0d..c0328b1435ce 100644
--- a/.github/workflows/java-bigtable-ci.yaml
+++ b/.github/workflows/java-bigtable-ci.yaml
@@ -137,8 +137,8 @@ jobs:
     - run: .kokoro/build.sh
       env:
         JOB_TYPE: lint
-        HEAD_SHA: ${{ github.event.pull_request.head.sha }}
-        BASE_SHA: ${{ github.event.pull_request.base.sha }}
+        HEAD_SHA: ${{ github.event.pull_request.head.sha || github.sha }}
+        BASE_SHA: ${{ github.event.pull_request.base.sha || github.event.before }}
   clirr:
     needs: filter
     if: ${{ needs.filter.outputs.library == 'true' }}
diff --git a/.github/workflows/java-pubsub-ci.yaml b/.github/workflows/java-pubsub-ci.yaml
index 5c87fa56c2f0..c4723c36b6f0 100644
--- a/.github/workflows/java-pubsub-ci.yaml
+++ b/.github/workflows/java-pubsub-ci.yaml
@@ -137,8 +137,8 @@ jobs:
     - run: .kokoro/build.sh
       env:
         JOB_TYPE: lint
-        HEAD_SHA: ${{ github.event.pull_request.head.sha }}
-        BASE_SHA: ${{ github.event.pull_request.base.sha }}
+        HEAD_SHA: ${{ github.event.pull_request.head.sha || github.sha }}
+        BASE_SHA: ${{ github.event.pull_request.base.sha || github.event.before }}
   clirr:
     needs: filter
     if: ${{ needs.filter.outputs.library == 'true' }}
diff --git a/.github/workflows/java-spanner-jdbc-ci.yaml b/.github/workflows/java-spanner-jdbc-ci.yaml
index 5d114841a7d2..4cbb5184193a 100644
--- a/.github/workflows/java-spanner-jdbc-ci.yaml
+++ b/.github/workflows/java-spanner-jdbc-ci.yaml
@@ -141,8 +141,8 @@ jobs:
     - run: .kokoro/build.sh
       env:
         JOB_TYPE: lint
-        HEAD_SHA: ${{ github.event.pull_request.head.sha }}
-        BASE_SHA: ${{ github.event.pull_request.base.sha }}
+        HEAD_SHA: ${{ github.event.pull_request.head.sha || github.sha }}
+        BASE_SHA: ${{ github.event.pull_request.base.sha || github.event.before }}
   required:
     needs: [ units, units-java8, windows, dependencies, javadoc, lint ]
     name: conditional-required-check
diff --git a/.github/workflows/java-storage-nio-ci.yaml b/.github/workflows/java-storage-nio-ci.yaml
index e53a05764dcb..efddd8ac27fd 100644
--- a/.github/workflows/java-storage-nio-ci.yaml
+++ b/.github/workflows/java-storage-nio-ci.yaml
@@ -141,8 +141,8 @@ jobs:
     - run: .kokoro/build.sh
       env:
         JOB_TYPE: lint
-        HEAD_SHA: ${{ github.event.pull_request.head.sha }}
-        BASE_SHA: ${{ github.event.pull_request.base.sha }}
+        HEAD_SHA: ${{ github.event.pull_request.head.sha || github.sha }}
+        BASE_SHA: ${{ github.event.pull_request.base.sha || github.event.before }}
   required:
     needs: [ units, units-java8, windows, dependencies, javadoc, lint ]
     name: conditional-required-check
diff --git a/generation/apply_versions.sh b/generation/apply_versions.sh
index 99d1ab3a3109..826d6df2213b 100755
--- a/generation/apply_versions.sh
+++ b/generation/apply_versions.sh
@@ -25,7 +25,7 @@ if [[ "$column_name" == "released" ]]; then
   column_index=2
 elif [[ "$column_name" == "current" ]]; then
   column_index=3
-elif "$column_name" != "current" ]]; then
+elif [[ "$column_name" != "current" ]]; then
   echo "Error: column_name must be either 'released' or 'current'"
   exit 1
 fi
diff --git a/generation/update_owlbot_postprocessor_config.sh b/generation/update_owlbot_postprocessor_config.sh
index a59d865bc2d9..275041f01305 100755
--- a/generation/update_owlbot_postprocessor_config.sh
+++ b/generation/update_owlbot_postprocessor_config.sh
@@ -6,7 +6,10 @@
 
 set -e
 
-for dir in $(find . -mindepth 2 -maxdepth 2 -name owlbot.py | grep -v 'java-common-protos/' | grep -v 'java-iam/' | grep -v 'java-showcase/' | sort | xargs dirname ); do
+TARGET_MODULE="${1:-.}"
+
+for owlbot_script in $(find "$TARGET_MODULE" -name owlbot.py | grep -v 'java-common-protos/' | grep -v 'java-iam/' | grep -v 'java-showcase/' | sort); do
+  dir=$(dirname "$owlbot_script")
   pushd "$dir"
 
   # form a perl command to replace java.common_templates() invocation
diff --git a/monorepo-migration/.gitignore b/monorepo-migration/.gitignore
new file mode 100644
index 000000000000..ae0b0d95a4b2
--- /dev/null
+++ b/monorepo-migration/.gitignore
@@ -0,0 +1,3 @@
+.git-filter-repo/
+__pycache__/
+*.pyc
diff --git a/monorepo-migration/migrate-bigtable.sh b/monorepo-migration/migrate-bigtable.sh
new file mode 100755
index 000000000000..076d93ec1b06
--- /dev/null
+++ b/monorepo-migration/migrate-bigtable.sh
@@ -0,0 +1,45 @@
+#!/bin/bash
+# Copyright 2026 Google LLC
+#
+# 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.
+
+# Exit on error
+set -e
+
+# Get absolute paths
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+MONOREPO_ROOT="$(dirname "$SCRIPT_DIR")"
+
+echo "========================================================"
+echo " Staging java-bigtable migration"
+echo "========================================================"
+
+# 1. Configure environment for the base migrate.sh script
+export SOURCE_REPO_URL="https://github.com/googleapis/java-bigtable"
+export MIGRATION_HEAD_BRANCH="main"
+export SQUASH_COMMITS="false"
+export CODEOWNER="@googleapis/bigtable-team" 
+export BOM_SUBSTITUTIONS="gapic-libraries-bom:google-cloud-monitoring-bom" 
+export PRE_INSTALL_DEPS="java-monitoring/google-cloud-monitoring-bom,java-monitoring/google-cloud-monitoring" 
+
+# 2. Execute the central migration script
+"${SCRIPT_DIR}/migrate.sh"
+
+echo ""
+echo "========================================================"
+echo "Migration staged successfully!"
+echo "Results are available in the isolated clone:"
+echo "  migration-work/google-cloud-java-target"
+echo "Current Branch: migrate-java-bigtable"
+echo "Next Steps: cd migration-work/google-cloud-java-target && mvn clean install -DskipTests"
+echo "========================================================"
diff --git a/monorepo-migration/migrate-firestore.sh b/monorepo-migration/migrate-firestore.sh
new file mode 100755
index 000000000000..babdce93fd58
--- /dev/null
+++ b/monorepo-migration/migrate-firestore.sh
@@ -0,0 +1,43 @@
+#!/bin/bash
+# Copyright 2026 Google LLC
+#
+# 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.
+
+# Exit on error
+set -e
+
+# Get absolute paths
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+MONOREPO_ROOT="$(dirname "$SCRIPT_DIR")"
+
+echo "========================================================"
+echo " Staging java-firestore migration"
+echo "========================================================"
+
+# 1. Configure environment for the base migrate.sh script
+export SOURCE_REPO_URL="https://github.com/googleapis/java-firestore"
+export MIGRATION_HEAD_BRANCH="main"
+export SQUASH_COMMITS="false"
+export CODEOWNER="@googleapis/firestore-team" 
+
+# 2. Execute the central migration script
+"${SCRIPT_DIR}/migrate.sh"
+
+echo ""
+echo "========================================================"
+echo "Migration staged successfully!"
+echo "Results are available in the isolated clone:"
+echo "  migration-work/google-cloud-java-target"
+echo "Current Branch: migrate-java-firestore"
+echo "Next Steps: cd migration-work/google-cloud-java-target && mvn clean install -DskipTests"
+echo "========================================================"
diff --git a/monorepo-migration/migrate-pubsub.sh b/monorepo-migration/migrate-pubsub.sh
new file mode 100755
index 000000000000..3d8a3d1cda54
--- /dev/null
+++ b/monorepo-migration/migrate-pubsub.sh
@@ -0,0 +1,46 @@
+#!/bin/bash
+# Copyright 2026 Google LLC
+#
+# 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.
+
+# Exit on error
+set -e
+
+# Get absolute paths
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+MONOREPO_ROOT="$(dirname "$SCRIPT_DIR")"
+
+echo "========================================================"
+echo " Staging java-pubsub migration"
+echo "========================================================"
+
+# 1. Configure environment for the base migrate.sh script
+export SOURCE_REPO_URL="https://github.com/googleapis/java-pubsub"
+export MIGRATION_HEAD_BRANCH="main"
+export SQUASH_COMMITS="false"
+export CODEOWNER="@googleapis/pubsub-team" 
+export SUREFIRE_JVM_OPT="-DskipTests"
+
+# 2. Execute the central migration script
+# This performs git read-tree, POM modernization, workflow transformation, and generation config updates.
+# Note: migrate.sh works in an isolated sibling clone to avoid polluting the active workspace.
+"${SCRIPT_DIR}/migrate.sh"
+
+echo ""
+echo "========================================================"
+echo "Migration staged successfully!"
+echo "Results are available in the isolated clone:"
+echo "  ../../migration-work/google-cloud-java-target"
+echo "Current Branch: migrate-java-pubsub"
+echo "Next Steps: cd ../../migration-work/google-cloud-java-target && mvn clean install -DskipTests"
+echo "========================================================"
diff --git a/monorepo-migration/migrate.sh b/monorepo-migration/migrate.sh
index 93b4b2c788c4..b4c795e0805d 100755
--- a/monorepo-migration/migrate.sh
+++ b/monorepo-migration/migrate.sh
@@ -17,6 +17,26 @@
 # Exit on error
 set -e
 
+# Get absolute path to the script directory
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+MONOREPO_ROOT="$(dirname "$SCRIPT_DIR")"
+
+# Ensure git-filter-repo is available in PATH
+if ! command -v git-filter-repo >/dev/null 2>&1; then
+    LOCAL_FILTER_REPO_DIR="${SCRIPT_DIR}/.git-filter-repo"
+    LOCAL_FILTER_REPO="${LOCAL_FILTER_REPO_DIR}/git-filter-repo"
+    
+    if [ ! -f "$LOCAL_FILTER_REPO" ]; then
+        echo "git-filter-repo not found locally or in PATH. Downloading version v2.45.0..."
+        mkdir -p "$LOCAL_FILTER_REPO_DIR"
+        curl -sSL -o "$LOCAL_FILTER_REPO" "https://raw.githubusercontent.com/newren/git-filter-repo/v2.45.0/git-filter-repo"
+        chmod +x "$LOCAL_FILTER_REPO"
+    fi
+    
+    echo "Injecting local .git-filter-repo into PATH..."
+    export PATH="${LOCAL_FILTER_REPO_DIR}:$PATH"
+fi
+
 # Function to check if a command exists
 check_command() {
     if ! command -v "$1" >/dev/null 2>&1; then
@@ -29,6 +49,7 @@ check_command() {
 check_command git
 check_command python3
 check_command mvn
+check_command git-filter-repo
 
 # Configuration
 MONOREPO_URL="https://github.com/googleapis/google-cloud-java"
@@ -42,13 +63,12 @@ CODEOWNER="${CODEOWNER:-}"
 SOURCE_REPO_NAME="${SOURCE_REPO_URL##*/}"
 MONOREPO_NAME="${MONOREPO_URL##*/}"
 
-# Use a temporary working directory sibling to the current monorepo
-WORKING_DIR="../../migration-work"
+# Use a temporary working directory sibling to the current monorepo, anchored to script location
+WORKING_DIR="$(cd "${SCRIPT_DIR}/../.." && pwd)/migration-work"
 SOURCE_DIR="$WORKING_DIR/$SOURCE_REPO_NAME-source"
 TARGET_DIR="$WORKING_DIR/$MONOREPO_NAME-target"
 
-# Get absolute path to the transformation script before any cd
-TRANSFORM_SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
+TRANSFORM_SCRIPT_DIR="${SCRIPT_DIR}"
 TRANSFORM_SCRIPT="$TRANSFORM_SCRIPT_DIR/transform_workflow.py"
 MODERNIZE_POM_SCRIPT="$TRANSFORM_SCRIPT_DIR/modernize_pom.py"
 UPDATE_ROOT_POM_SCRIPT="$TRANSFORM_SCRIPT_DIR/update_root_pom.py"
@@ -56,6 +76,10 @@ FIX_COPYRIGHT_SCRIPT="$TRANSFORM_SCRIPT_DIR/fix_copyright_headers.py"
 UPDATE_GENERATION_CONFIG_SCRIPT="$TRANSFORM_SCRIPT_DIR/update_generation_config.py"
 UPDATE_OWLBOT_HERMETIC_SCRIPT="$TRANSFORM_SCRIPT_DIR/update_owlbot_hermetic.py"
 TRANSFORM_OWLBOT_SCRIPT="$TRANSFORM_SCRIPT_DIR/update_owlbot.py"
+UPDATE_SAMPLES_BUILD_SCRIPT="$TRANSFORM_SCRIPT_DIR/update_samples_build.py"
+UPDATE_LINTER_EXCLUSIONS_SCRIPT="$TRANSFORM_SCRIPT_DIR/update_linter_exclusions.py"
+UPDATE_CI_FILTERS_SCRIPT="$TRANSFORM_SCRIPT_DIR/update_ci_filters.py"
+UPDATE_CHANGES_FILTERS_SCRIPT="$TRANSFORM_SCRIPT_DIR/update_changes_filters.py"
 
 # Track number of commits made by this script
 COMMIT_COUNT=0
@@ -65,23 +89,28 @@ echo "Starting migration using git read-tree with isolated clones..."
 # 0. Create working directory
 mkdir -p "$WORKING_DIR"
 
-MIGRATION_HEAD_BRANCH="${MIGRATION_HEAD_BRANCH:-main}"
+MIGRATION_HEAD_BRANCH="main"
 echo "Basing migration branch on: ${MIGRATION_HEAD_BRANCH}"
 
 # 1. Clone the source repository
-if [ ! -d "$SOURCE_DIR" ]; then
-    echo "Cloning source repo: $SOURCE_REPO_URL into $SOURCE_DIR"
-    git clone "$SOURCE_REPO_URL" "$SOURCE_DIR"
+if [ "${SKIP_SOURCE_UPDATE:-false}" = "true" ] && [ -d "$SOURCE_DIR" ]; then
+    echo "Skipping source repository update and reusing existing directory..."
 else
-    echo "Source directory $SOURCE_DIR already exists. Ensuring it is clean and up-to-date..."
+    echo "Ensuring clean slate for history filters by removing existing source directory..."
+    rm -rf "$SOURCE_DIR"
+    echo "Cloning source repo: $SOURCE_REPO_URL into $SOURCE_DIR"
+    git clone --branch main --single-branch "$SOURCE_REPO_URL" "$SOURCE_DIR"
+fi
+
+if [ "${SKIP_SOURCE_UPDATE:-false}" != "true" ]; then
+    # 1.2 Rewrite history of the split repo to move files to the target subdirectory
+    echo "Moving files to destination path: ${SOURCE_REPO_NAME} in history..."
     cd "$SOURCE_DIR"
-    git fetch origin
-    git checkout -f "main"
-    git reset --hard origin/main
-    git clean -fd
+    git filter-repo --to-subdirectory-filter "${SOURCE_REPO_NAME}" --force
     cd - > /dev/null
 fi
 
+
 # 1.5 Extract CODEOWNERS from source repository as default
 if [ -z "$CODEOWNER" ]; then
     echo "Attempting to find default CODEOWNER from source repository..."
@@ -114,28 +143,30 @@ fi
 # 2. Clone the target monorepo (the "isolated clone")
 if [ ! -d "$TARGET_DIR" ]; then
     echo "Cloning target monorepo: $MONOREPO_URL into $TARGET_DIR"
-    git clone "$MONOREPO_URL" "$TARGET_DIR"
-    git checkout -f "${MIGRATION_HEAD_BRANCH}"
-    git reset --hard origin/${MIGRATION_HEAD_BRANCH}
+    git clone --branch main --single-branch --depth 1 "$MONOREPO_URL" "$TARGET_DIR"
 else
     echo "Target directory $TARGET_DIR already exists. Ensuring it is clean and up-to-date..."
     cd "$TARGET_DIR"
-    git fetch origin
-    git checkout -f "${MIGRATION_HEAD_BRANCH}"
-    git reset --hard origin/${MIGRATION_HEAD_BRANCH}
+    git fetch --depth 1 origin main
+    git checkout -f "main"
+    git reset --hard origin/main
     git clean -fd
     cd - > /dev/null
 fi
 
 cd "$TARGET_DIR"
+if [ "$(pwd)" = "$MONOREPO_ROOT" ]; then
+    echo "CRITICAL ERROR: Script failed to change directory or attempted to run destructive Git operations inside the active workspace!" >&2
+    exit 1
+fi
 
 # Ensure we are on a clean main branch in the target clone
 echo "Ensuring clean state in target monorepo..."
-git fetch origin
+git fetch --depth 1 origin main
 git reset --hard HEAD
 git clean -fd
-git checkout -f "${MIGRATION_HEAD_BRANCH}"
-git reset --hard origin/${MIGRATION_HEAD_BRANCH}
+git checkout -f "main"
+git reset --hard origin/main
 git clean -fdx
 
 # Check if the repository is already migrated
@@ -165,13 +196,119 @@ git remote add "$SOURCE_REPO_NAME" "../$SOURCE_REPO_NAME-source"
 echo "Fetching $SOURCE_REPO_NAME..."
 git fetch "$SOURCE_REPO_NAME"
 
-# 5. Merge the histories using 'ours' strategy to keep monorepo content
-echo "Merging histories (strategy: ours)..."
-git merge --allow-unrelated-histories --no-ff "$SOURCE_REPO_NAME/main" -s ours --no-commit -m "chore($SOURCE_REPO_NAME): migrate $SOURCE_REPO_NAME into monorepo"
+# 5. Merge the histories to pull all rewritten files into their subdirectory directly
+echo "Merging histories..."
+git merge --allow-unrelated-histories --no-edit --no-gpg-sign "$SOURCE_REPO_NAME/main" -m "chore($SOURCE_REPO_NAME): migrate $SOURCE_REPO_NAME into monorepo"
+COMMIT_COUNT=$((COMMIT_COUNT + 1))
+
+# 6.4b Migrate GraalVM Native presubmit config if present
+if [ -f "$SOURCE_REPO_NAME/.kokoro/presubmit/graalvm-native-a.cfg" ]; then
+    echo "Migrating graalvm-native-a.cfg to monorepo root .kokoro/presubmit/${SOURCE_REPO_NAME#java-}-graalvm-native-presubmit.cfg..."
+    mkdir -p .kokoro/presubmit
+    sed -e 's/value: "graalvm"/value: "graalvm-single"/' \
+        "$SOURCE_REPO_NAME/.kokoro/presubmit/graalvm-native-a.cfg" > ".kokoro/presubmit/${SOURCE_REPO_NAME#java-}-graalvm-native-presubmit.cfg"
+    
+    # Append BUILD_SUBDIR
+    cat <<EOF >> ".kokoro/presubmit/${SOURCE_REPO_NAME#java-}-graalvm-native-presubmit.cfg"
+
+env_vars: {
+  key: "BUILD_SUBDIR"
+  value: "${SOURCE_REPO_NAME}"
+}
+EOF
+    git add ".kokoro/presubmit/${SOURCE_REPO_NAME#java-}-graalvm-native-presubmit.cfg"
+    git commit -n --no-gpg-sign -m "chore($SOURCE_REPO_NAME): migrate GraalVM Native presubmit config"
+    COMMIT_COUNT=$((COMMIT_COUNT + 1))
+fi
+
+# 6.4c Migrate Integration presubmit configurations if present
+if ls "$SOURCE_REPO_NAME/.kokoro/presubmit/integration"*.cfg >/dev/null 2>&1; then
+    mkdir -p .kokoro/presubmit
+    for cfg_file in "$SOURCE_REPO_NAME/.kokoro/presubmit/integration"*.cfg; do
+        if [ -f "$cfg_file" ]; then
+            filename=$(basename "$cfg_file")
+            new_filename="${filename/integration/${SOURCE_REPO_NAME#java-}-integration}"
+            target_cfg=".kokoro/presubmit/${new_filename}"
+            
+            echo "Migrating and adapting $filename to $target_cfg..."
+            sed -e 's/value: "integration"/value: "integration-single"/' \
+                -e 's/java8/java11/' \
+                "$cfg_file" > "$target_cfg"
+            
+            # Append BUILD_SUBDIR
+            cat <<EOF >> "$target_cfg"
+
+env_vars: {
+  key: "BUILD_SUBDIR"
+  value: "${SOURCE_REPO_NAME}"
+}
+EOF
+            git add "$target_cfg"
+        fi
+    done
+    git commit -n --no-gpg-sign -m "chore($SOURCE_REPO_NAME): migrate Integration presubmit configurations"
+    COMMIT_COUNT=$((COMMIT_COUNT + 1))
+fi
+
+# 6.4c(2) Migrate custom conformance execution script if present
+if [ -f "$SOURCE_REPO_NAME/.kokoro/conformance.sh" ]; then
+    echo "Migrating conformance.sh to monorepo root .kokoro/${SOURCE_REPO_NAME#java-}-conformance.sh..."
+    mkdir -p .kokoro
+    cp "$SOURCE_REPO_NAME/.kokoro/conformance.sh" ".kokoro/${SOURCE_REPO_NAME#java-}-conformance.sh"
+    echo "Adapting conformance script paths and build scopes for monorepo root..."
+    
+    # 1. Append popd to the end of the original install block (-T 1C)
+    sed -i.bak 's|-T 1C|-T 1C\n  popd|' ".kokoro/${SOURCE_REPO_NAME#java-}-conformance.sh"
+    
+    # 2. Construct the unified pre-installation block and pushd subdirectory scoping
+    if [ -n "${PRE_INSTALL_DEPS}" ]; then
+        PRE_INSTALL_BLOCK="echo \"Installing toolchain and external prerequisites recursively using monorepo install_modules...\"\ninstall_modules \"${PRE_INSTALL_DEPS}\"\n"
+    else
+        PRE_INSTALL_BLOCK="echo \"Installing platform toolchain recursively using monorepo install_modules...\"\ninstall_modules\n"
+    fi
+    PRE_INSTALL_BLOCK="${PRE_INSTALL_BLOCK}\npushd ${SOURCE_REPO_NAME}\n# attempt to install 3 times"
+    
+    # 3. Inject the pre-installation and pushd block
+    sed -i.bak "s|# attempt to install 3 times|${PRE_INSTALL_BLOCK}|" ".kokoro/${SOURCE_REPO_NAME#java-}-conformance.sh"
+    
+    # 4. Adapt other paths to monorepo root
+    sed -i.bak "s|cd test-proxy|cd ${SOURCE_REPO_NAME}/test-proxy|" ".kokoro/${SOURCE_REPO_NAME#java-}-conformance.sh"
+    sed -i.bak "s|-jar test-proxy/target/|-jar ${SOURCE_REPO_NAME}/test-proxy/target/|" ".kokoro/${SOURCE_REPO_NAME#java-}-conformance.sh"
+    sed -i.bak "s|kill \${proxyPID}|kill \${proxyPID} \&\& sleep 5|" ".kokoro/${SOURCE_REPO_NAME#java-}-conformance.sh"
+    sed -i.bak "s|../../test-proxy/known_failures.txt|../../${SOURCE_REPO_NAME}/test-proxy/known_failures.txt|" ".kokoro/${SOURCE_REPO_NAME#java-}-conformance.sh"
+    sed -i.bak 's|mvn install -B -V|mvn install -U -B -V|' ".kokoro/${SOURCE_REPO_NAME#java-}-conformance.sh"
+    sed -i.bak 's|mvn clean install -DskipTests|mvn clean install -U -DskipTests|' ".kokoro/${SOURCE_REPO_NAME#java-}-conformance.sh"
+    rm -f ".kokoro/${SOURCE_REPO_NAME#java-}-conformance.sh.bak"
+    
+    if [ -f "${SOURCE_REPO_NAME}/test-proxy/pom.xml" ]; then
+        echo "Fixing protoc-gen-grpc-java version in test-proxy/pom.xml for Apple Silicon (osx-aarch_64) support..."
+        sed -i.bak "s|1.24.0:exe:\${os.detected.classifier}|1.62.2:exe:\${os.detected.classifier}|" "${SOURCE_REPO_NAME}/test-proxy/pom.xml"
+        rm -f "${SOURCE_REPO_NAME}/test-proxy/pom.xml.bak"
+        
+        echo "Patching monorepo core .kokoro/build.sh inside target clone to exclude test-proxy from changed-modules linting..."
+        sed -i.bak 's|unmanaged-dependency-check" \]\] \&\& \\|unmanaged-dependency-check" \]\] \&\& \\\n                       \[\[ "$(basename "${dir}")" != \*"test-proxy"\* \]\] \&\& \\|' ".kokoro/build.sh"
+        rm -f ".kokoro/build.sh.bak"
+        
+        git add "${SOURCE_REPO_NAME}/test-proxy/pom.xml" ".kokoro/build.sh"
+        git commit -n --no-gpg-sign -m "chore($SOURCE_REPO_NAME): fix test-proxy compilation and exclude from linter changes matrix"
+        COMMIT_COUNT=$((COMMIT_COUNT + 1))
+    fi
+    
+    git add ".kokoro/${SOURCE_REPO_NAME#java-}-conformance.sh"
+    git commit -n --no-gpg-sign -m "chore($SOURCE_REPO_NAME): migrate and adapt conformance execution script"
+    COMMIT_COUNT=$((COMMIT_COUNT + 1))
+fi
 
-# 6. Read the tree from the source repo into the desired subdirectory
-echo "Reading tree into prefix $SOURCE_REPO_NAME/..."
-git read-tree --prefix="$SOURCE_REPO_NAME/" -u "$SOURCE_REPO_NAME/main"
+# 6.4d Update repo and repo_short in .repo-metadata.json
+REPO_METADATA="$SOURCE_REPO_NAME/.repo-metadata.json"
+if [ -f "$REPO_METADATA" ]; then
+    echo "Updating repo and repo_short in $REPO_METADATA..."
+    python3 -c "import json; f = '$REPO_METADATA'; d = json.load(open(f)); d['repo'] = 'googleapis/google-cloud-java'; json.dump(d, open(f, 'w'), indent=2); open(f, 'a').write('\n')"
+    
+    git add "$REPO_METADATA"
+    git commit -n --no-gpg-sign -m "chore($SOURCE_REPO_NAME): update .repo-metadata.json"
+    COMMIT_COUNT=$((COMMIT_COUNT + 1))
+fi
 
 # 6.5 Remove common files from the root of the migrated library
 echo "Removing common files from the root of $SOURCE_REPO_NAME/..."
@@ -180,16 +317,14 @@ rm -f "$SOURCE_REPO_NAME/renovate.json"
 rm -f "$SOURCE_REPO_NAME/LICENSE"
 rm -f "$SOURCE_REPO_NAME/java.header"
 rm -rf "$SOURCE_REPO_NAME/.kokoro"
-# rm -rf "$SOURCE_REPO_NAME/.kokoro/continuous"  "$SOURCE_REPO_NAME/.kokoro/nightly"  "$SOURCE_REPO_NAME/.kokoro/presubmit"
 rm -f "$SOURCE_REPO_NAME/codecov.yaml"
 rm -f "$SOURCE_REPO_NAME/synth.metadata"
 rm -f "$SOURCE_REPO_NAME/license-checks.xml"
-find "$SOURCE_REPO_NAME" -maxdepth 1 -name "*.md" ! -name "CHANGELOG.md" ! -name "README.md" -delete
+find "$SOURCE_REPO_NAME" -maxdepth 1 -name "*.md" ! -name "CHANGELOG.md" ! -name "README.md" ! -name "GEMINI.md" ! -name "DEVELOPMENT.md" -delete
 
-# 7. Commit the migration
-echo "Committing migration..."
+echo "Committing removal of common files..."
 git add "$SOURCE_REPO_NAME"
-git commit -n --no-gpg-sign -m "chore($SOURCE_REPO_NAME): migrate $SOURCE_REPO_NAME into monorepo"
+git commit -n --no-gpg-sign -m "chore($SOURCE_REPO_NAME): remove common files from module root"
 COMMIT_COUNT=$((COMMIT_COUNT + 1))
 
 # 7.1 Update CODEOWNERS
@@ -227,7 +362,7 @@ if [ -d "$SOURCE_REPO_NAME/.github/workflows" ]; then
             case "$filename" in
                 "hermetic_library_generation.yaml" | "update_generation_config.yaml" | \
                 "approve-readme.yaml" | "auto-release.yaml" | "renovate_config_check.yaml" | \
-                "samples.yaml" | "unmanaged_dependency_check.yaml")
+                "samples.yaml" | "unmanaged_dependency_check.yaml" | "unmanaged-dependency-check.yaml")
                     echo "Skipping redundant workflow: $filename"
                     continue
                     ;;
@@ -238,6 +373,10 @@ if [ -d "$SOURCE_REPO_NAME/.github/workflows" ]; then
             
             echo "Migrating and adapting $filename to $target_path"
             python3 "$TRANSFORM_SCRIPT" "$SOURCE_REPO_NAME" < "$workflow" > "$target_path"
+            sed -i.bak "s|java-version: 8|java-version: 11|" "$target_path"
+            sed -i.bak "s|github.event.pull_request.head.sha|github.event.pull_request.head.sha \|\| github.sha|g" "$target_path"
+            sed -i.bak "s|github.event.pull_request.base.sha|github.event.pull_request.base.sha \|\| github.event.before|g" "$target_path"
+            rm -f "${target_path}.bak"
         fi
     done
     
@@ -251,6 +390,18 @@ if [ -d "$SOURCE_REPO_NAME/.github/workflows" ]; then
     COMMIT_COUNT=$((COMMIT_COUNT + 1))
 fi
 
+# 7.5b Adapt samples_build.yaml if present
+SAMPLES_BUILD_YAML="$SOURCE_REPO_NAME/.cloudbuild/samples_build.yaml"
+if [ -f "$SAMPLES_BUILD_YAML" ]; then
+    echo "Adapting samples_build.yaml..."
+    python3 "$UPDATE_SAMPLES_BUILD_SCRIPT" "$SAMPLES_BUILD_YAML" "$SOURCE_REPO_NAME"
+    
+    echo "Committing samples_build.yaml update..."
+    git add "$SAMPLES_BUILD_YAML"
+    git commit -n --no-gpg-sign -m "chore($SOURCE_REPO_NAME): adapt samples_build.yaml for monorepo"
+    COMMIT_COUNT=$((COMMIT_COUNT + 1))
+fi
+
 # 7.6 Update generation_config.yaml
 echo "Updating generation_config.yaml..."
 SOURCE_CONFIG="$SOURCE_REPO_NAME/generation_config.yaml"
@@ -284,8 +435,8 @@ fi
 
 # 7.8 Migrate .OwlBot-hermetic.yaml
 echo "Migrating .OwlBot-hermetic.yaml..."
-if [ -f "$SOURCE_DIR/.github/.OwlBot-hermetic.yaml" ]; then
-    SOURCE_OWLBOT="$SOURCE_DIR/.github/.OwlBot-hermetic.yaml"
+if [ -f "$SOURCE_DIR/$SOURCE_REPO_NAME/.github/.OwlBot-hermetic.yaml" ]; then
+    SOURCE_OWLBOT="$SOURCE_DIR/$SOURCE_REPO_NAME/.github/.OwlBot-hermetic.yaml"
 else
     SOURCE_OWLBOT=""
 fi
@@ -303,10 +454,10 @@ fi
 
 # 7.8b Migrate owlbot.py
 echo "Migrating owlbot.py..."
-if [ -f "$SOURCE_DIR/owlbot.py" ]; then
+if [ -f "$SOURCE_DIR/$SOURCE_REPO_NAME/owlbot.py" ]; then
     TARGET_OWLBOT="$SOURCE_REPO_NAME/owlbot.py"
     
-    python3 "$TRANSFORM_OWLBOT_SCRIPT" "$TARGET_OWLBOT" "$SOURCE_DIR/owlbot.py"
+    python3 "$TRANSFORM_OWLBOT_SCRIPT" "$TARGET_OWLBOT" "$SOURCE_DIR/$SOURCE_REPO_NAME/owlbot.py"
 
     echo "Committing owlbot.py migration..."
     git add "$TARGET_OWLBOT"
@@ -348,10 +499,54 @@ while read -r bom_pom; do
     COMMIT_COUNT=$((COMMIT_COUNT + 1))
 done < <(find "$SOURCE_REPO_NAME" -name "pom.xml" | grep "\-bom/pom.xml" | grep -v "samples")
 
+# 7.12b Align all version markers across the monorepo
+echo "Aligning all version markers using apply_versions.sh..."
+bash generation/apply_versions.sh versions.txt current
+
+# 7.12c Sync all owlbot.py formatting
+echo "Syncing all owlbot.py formatting..."
+bash generation/update_owlbot_postprocessor_config.sh "$SOURCE_REPO_NAME" || true
+
+git add -u
+git commit -n --no-gpg-sign -m "chore($SOURCE_REPO_NAME): align versions and format owlbot configurations"
+COMMIT_COUNT=$((COMMIT_COUNT + 1))
+
+# 7.8c Exempt module from global integration testing matrix
+echo "Exempting $SOURCE_REPO_NAME from global integration testing matrix..."
+sed -i.bak "s/'java-storage-nio'/'java-storage-nio'\n  '${SOURCE_REPO_NAME}'/" ".kokoro/common.sh"
+python3 "$UPDATE_CI_FILTERS_SCRIPT" ".github/workflows/ci.yaml" "$SOURCE_REPO_NAME"
+python3 "$UPDATE_CHANGES_FILTERS_SCRIPT" ".github/workflows/ci.yaml" "$SOURCE_REPO_NAME"
+
+if [ -n "${PRE_INSTALL_DEPS}" ]; then
+    echo "Injecting explicit dependencies into always_install_deps list inside .kokoro/common.sh..."
+    for dep in $(echo "${PRE_INSTALL_DEPS}" | tr ',' ' '); do
+        sed -i.bak "s|always_install_deps_list=(|always_install_deps_list=(\n      '${dep}'|" ".kokoro/common.sh"
+    done
+    rm -f .kokoro/common.sh.bak
+fi
+
+echo "Committing common.sh and ci.yaml updates..."
+git add .kokoro/common.sh .github/workflows/ci.yaml
+git commit -n --no-gpg-sign -m "chore($SOURCE_REPO_NAME): exempt from global integration testing matrix"
+COMMIT_COUNT=$((COMMIT_COUNT + 1))
+
+# 7.9b Conditionally skip version check if unmanaged dependencies exist
+echo "Verifying non-release-please version compliance..."
+if ! (./generation/check_non_release_please_versions.sh > /dev/null 2>&1); then
+    echo "Unmanaged dependency versions detected. Injecting $SOURCE_REPO_NAME exclusion into check_non_release_please_versions.sh..."
+    python3 "$UPDATE_LINTER_EXCLUSIONS_SCRIPT" "generation/check_non_release_please_versions.sh" "$SOURCE_REPO_NAME"
+    
+    echo "Committing linter adjustment..."
+    git add generation/check_non_release_please_versions.sh
+    git commit -n --no-gpg-sign -m "chore($SOURCE_REPO_NAME): skip version check for $SOURCE_REPO_NAME"
+    COMMIT_COUNT=$((COMMIT_COUNT + 1))
+else
+    echo "All dependency versions fully managed. No linter adjustments required."
+fi
+
 # 7.11 Verify compilation
 echo "Verifying compilation..."
 BUILD_SUBDIR="${SOURCE_REPO_NAME}" JOB_TYPE=test .kokoro/build.sh
-# (cd "$SOURCE_REPO_NAME" && mvn compile -DskipTests -T 1C)
 
 # 7.13 Squash commits
 if [ "${SQUASH_COMMITS:-false}" = "true" ]; then
@@ -376,8 +571,10 @@ if [ "${SQUASH_COMMITS:-false}" = "true" ]; then
 fi
 
 # 8. Cleanup
-echo "Cleaning up temporary source clone..."
-rm -rf "$SOURCE_DIR"
+if [ "${SKIP_SOURCE_UPDATE:-false}" != "true" ]; then
+    echo "Cleaning up temporary source clone..."
+    rm -rf "$SOURCE_DIR"
+fi
 
 echo "Migration complete!"
 echo "The migrated codebase is available in: $TARGET_DIR"
diff --git a/monorepo-migration/migrate_issues.sh b/monorepo-migration/migrate_issues.sh
new file mode 100755
index 000000000000..373f0ebe2639
--- /dev/null
+++ b/monorepo-migration/migrate_issues.sh
@@ -0,0 +1,129 @@
+#!/bin/bash
+# Copyright 2026 Google LLC
+#
+# 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.
+
+# migrate_issues.sh - Transfer open GitHub issues from one repo to another using gh CLI.
+
+set -e
+
+usage() {
+  echo "Usage: $0 <source-repo> <target-repo> [--label <label>] [--dry-run]"
+  echo "Example: $0 googleapis/python-storage googleapis/google-cloud-python --label 'api: storage'"
+  exit 1
+}
+
+if [[ $# -lt 2 ]]; then
+  usage
+fi
+
+SOURCE_REPO=$1
+TARGET_REPO=$2
+shift 2
+
+DRY_RUN=false
+REQUIRED_LABEL=""
+
+while [[ "$#" -gt 0 ]]; do
+  case $1 in
+    --dry-run) DRY_RUN=true; shift ;;
+    --label) REQUIRED_LABEL="$2"; shift 2 ;;
+    *) echo "Unknown parameter passed: $1"; usage ;;
+  esac
+done
+
+# Check if gh is installed
+if ! command -v gh &> /dev/null; then
+  echo "Error: gh (GitHub CLI) is not installed."
+  exit 1
+fi
+
+# Check if authenticated
+if ! gh auth status &> /dev/null; then
+  echo "Error: gh is not authenticated. Run 'gh auth login' first."
+  exit 1
+fi
+
+echo "Transferring open issues from $SOURCE_REPO to $TARGET_REPO..."
+if [ "$DRY_RUN" = true ]; then
+  echo "--- DRY RUN MODE ---"
+fi
+
+# Ensure label exists in target repo
+if [[ -n "$REQUIRED_LABEL" ]]; then
+  echo "Ensuring label '$REQUIRED_LABEL' exists in $TARGET_REPO..."
+  if ! gh label list --repo "$TARGET_REPO" --limit 1000 --json name --jq '.[].name' | grep -Fxq "$REQUIRED_LABEL"; then
+    if [ "$DRY_RUN" = true ]; then
+      echo "  [DRY RUN] Would create label '$REQUIRED_LABEL' in $TARGET_REPO"
+    else
+      echo "  Creating label '$REQUIRED_LABEL' in $TARGET_REPO..."
+      gh label create "$REQUIRED_LABEL" --repo "$TARGET_REPO" --color "ededed"
+    fi
+  else
+    echo "  Label '$REQUIRED_LABEL' already exists."
+  fi
+fi
+
+# Fetch all open issues from source repo
+# We use --limit 1000 to get a reasonable amount of issues. Adjust if needed.
+ISSUE_NUMBERS=$(gh issue list --repo "$SOURCE_REPO" --state open --limit 1000 --json number --jq '.[].number')
+
+if [[ -z "$ISSUE_NUMBERS" ]]; then
+  echo "No open issues found in $SOURCE_REPO."
+  exit 0
+fi
+
+# Extract short name from SOURCE_REPO (e.g., java-bigquery from googleapis/java-bigquery)
+REPO_SHORT_NAME=$(echo "$SOURCE_REPO" | cut -d'/' -f2)
+
+# Process each issue
+for ISSUE_NUMBER in $ISSUE_NUMBERS; do
+  echo "Processing Issue #$ISSUE_NUMBER..."
+
+  # Get the current title
+  TITLE=$(gh issue view "$ISSUE_NUMBER" --repo "$SOURCE_REPO" --json title --jq '.title')
+  NEW_TITLE="[$REPO_SHORT_NAME] $TITLE"
+
+  if [ "$DRY_RUN" = true ]; then
+    echo "  [DRY RUN] Would transfer #$ISSUE_NUMBER to $TARGET_REPO"
+    echo "  [DRY RUN] Would update title to: $NEW_TITLE"
+    if [[ -n "$REQUIRED_LABEL" ]]; then
+      echo "  [DRY RUN] Would add label '$REQUIRED_LABEL' to transferred issue"
+    fi
+  else
+    echo "  Transferring #$ISSUE_NUMBER..."
+    # Capture the output of transfer to get the new issue URL
+    TRANSFER_OUTPUT=$(gh issue transfer "$ISSUE_NUMBER" "$TARGET_REPO" --repo "$SOURCE_REPO")
+    
+    # The output is typically something like: https://github.com/googleapis/google-cloud-java/issues/1234
+    NEW_ISSUE_URL=$(echo "$TRANSFER_OUTPUT" | grep -o 'https://github.com/[^ ]*')
+    NEW_ISSUE_NUMBER=$(echo "$NEW_ISSUE_URL" | awk -F'/' '{print $NF}')
+
+    if [[ -n "$NEW_ISSUE_NUMBER" ]]; then
+      echo "  Transferred to $TARGET_REPO as #$NEW_ISSUE_NUMBER. Updating issue..."
+      
+      # Prepare edit command arguments
+      EDIT_ARGS=("--title" "$NEW_TITLE")
+      if [[ -n "$REQUIRED_LABEL" ]]; then
+        EDIT_ARGS+=("--add-label" "$REQUIRED_LABEL")
+      fi
+      
+      gh issue edit "$NEW_ISSUE_NUMBER" --repo "$TARGET_REPO" "${EDIT_ARGS[@]}"
+      echo "  Issue updated."
+    else
+      echo "  Warning: Could not determine new issue number from output: $TRANSFER_OUTPUT"
+    fi
+  fi
+done
+
+echo "Transfer completed."
\ No newline at end of file
diff --git a/monorepo-migration/modernize_pom.py b/monorepo-migration/modernize_pom.py
index bb8268c42470..7b2056badbd8 100644
--- a/monorepo-migration/modernize_pom.py
+++ b/monorepo-migration/modernize_pom.py
@@ -85,7 +85,7 @@ def get_monorepo_versions(monorepo_root='.'):
     versions = {}
     for root, dirs, files in os.walk(monorepo_root):
         # Skip common directories to improve performance and avoid noise
-        dirs[:] = [d for d in dirs if d not in ['samples', 'test', 'target', '.git', '.cloud', 'verification', 'test_data']]
+        dirs[:] = [d for d in dirs if d not in ['samples', 'test', 'target', '.git', '.cloud', 'verification', 'test_data', 'generation']]
         
         if 'pom.xml' in files:
             pom_path = os.path.join(root, 'pom.xml')
@@ -95,6 +95,16 @@ def get_monorepo_versions(monorepo_root='.'):
     return versions
 
 def modernize_pom(file_path, parent_version, source_repo_name=None, parent_artifactId='google-cloud-jar-parent', relative_path='../google-cloud-jar-parent/pom.xml', monorepo_versions=None):
+    bom_substitutions_env = os.environ.get('BOM_SUBSTITUTIONS')
+    bom_substitutions = {}
+    if bom_substitutions_env:
+        for pair in bom_substitutions_env.split(','):
+            if ':' in pair:
+                old, new = pair.split(':', 1)
+                bom_substitutions[old.strip()] = new.strip()
+                
+    is_root_pom = source_repo_name and file_path.endswith(f"{source_repo_name}/pom.xml")
+
     with open(file_path, 'r') as f:
         lines = f.readlines()
 
@@ -182,12 +192,30 @@ def modernize_pom(file_path, parent_version, source_repo_name=None, parent_artif
                     current_group_id = None
                     current_artifact_id = None
                     has_version = False
+                    in_exclusions = False
                     continue
                 if '</dependency>' in line:
                     in_dependency = False
                     current_dependency_lines.append(line)
 
-                    if current_artifact_id == 'google-cloud-shared-dependencies':
+                    if current_artifact_id == 'google-cloud-shared-dependencies' and '-deps-bom' not in file_path:
+                        continue
+                        
+                    if current_artifact_id in bom_substitutions:
+                        target_bom = bom_substitutions[current_artifact_id]
+                        target_version = monorepo_versions.get(target_bom, '0.0.1-SNAPSHOT')
+                        target_marker = target_bom.replace('-bom', '')
+                        indent = "      "
+                        current_dependency_lines = [
+                            f"{indent}<dependency>\n",
+                            f"{indent}  <groupId>com.google.cloud</groupId>\n",
+                            f"{indent}  <artifactId>{target_bom}</artifactId>\n",
+                            f"{indent}  <version>{target_version}</version><!-- {{x-version-update:{target_marker}:current}} -->\n",
+                            f"{indent}  <type>pom</type>\n",
+                            f"{indent}  <scope>import</scope>\n",
+                            f"{indent}</dependency>\n"
+                        ]
+                        new_lines.extend(current_dependency_lines)
                         continue
 
                     # Preservation logic:
@@ -196,22 +224,29 @@ def modernize_pom(file_path, parent_version, source_repo_name=None, parent_artif
                     # 3. Is com.google.cloud group AND artifactId starts with google-cloud- AND has a version tag
                     is_external = current_group_id and not current_group_id.startswith('com.google')
                     is_google_cloud_lib = current_group_id == 'com.google.cloud' and current_artifact_id and current_artifact_id.startswith('google-cloud-')
+                    is_truth = current_group_id and current_group_id.startswith('com.google.truth')
                     
-                    if should_preserve or (is_external and has_version) or (is_google_cloud_lib and has_version):
+                    if should_preserve or (is_external and has_version) or (is_google_cloud_lib and has_version) or (is_truth and has_version):
                         new_lines.extend(current_dependency_lines)
                     continue
 
                 if in_dependency:
-                    if '<groupId>' in line:
-                        match = re.search(r'<groupId>(.*?)</groupId>', line)
-                        if match:
-                            current_group_id = match.group(1).strip()
-                    if '<artifactId>' in line:
-                        match = re.search(r'<artifactId>(.*?)</artifactId>', line)
-                        if match:
-                            current_artifact_id = match.group(1).strip()
-                    if '<version>' in line:
-                        has_version = True
+                    if '<exclusions>' in line:
+                        in_exclusions = True
+                    if '</exclusions>' in line:
+                        in_exclusions = False
+                        
+                    if not in_exclusions:
+                        if '<groupId>' in line:
+                            match = re.search(r'<groupId>(.*?)</groupId>', line)
+                            if match:
+                                current_group_id = match.group(1).strip()
+                        if '<artifactId>' in line:
+                            match = re.search(r'<artifactId>(.*?)</artifactId>', line)
+                            if match:
+                                current_artifact_id = match.group(1).strip()
+                        if '<version>' in line:
+                            has_version = True
                     
                     if monorepo_versions and current_artifact_id and current_artifact_id in monorepo_versions:
                         new_version = monorepo_versions[current_artifact_id]
@@ -247,6 +282,47 @@ def modernize_pom(file_path, parent_version, source_repo_name=None, parent_artif
 
         new_lines.append(line)
 
+    # Add bulkTests profile if it does not already exist (only for the library root pom.xml)
+    if is_root_pom:
+        bulk_tests_pattern = r'<id>\s*bulkTests\s*</id>'
+        if not re.search(bulk_tests_pattern, "".join(new_lines)):
+            in_profiles = False
+            inserted = False
+            for i in range(len(new_lines)):
+                if '<profiles>' in new_lines[i]:
+                    in_profiles = True
+                if '</profiles>' in new_lines[i] and in_profiles:
+                    indent = "    "
+                    profile_block = (
+                        f"{indent}<profile>\n"
+                        f"{indent}  <id>bulkTests</id>\n"
+                        f"{indent}  <properties>\n"
+                        f"{indent}    <skipTests>true</skipTests>\n"
+                        f"{indent}  </properties>\n"
+                        f"{indent}</profile>\n"
+                    )
+                    new_lines.insert(i, profile_block)
+                    inserted = True
+                    break
+            
+            # If no <profiles> section existed, create one before </project>
+            if not inserted:
+                for i in range(len(new_lines) - 1, -1, -1):
+                    if '</project>' in new_lines[i]:
+                        indent = "  "
+                        profile_block = (
+                            f"\n{indent}<profiles>\n"
+                            f"{indent}  <profile>\n"
+                            f"{indent}    <id>bulkTests</id>\n"
+                            f"{indent}    <properties>\n"
+                            f"{indent}      <skipTests>true</skipTests>\n"
+                            f"{indent}    </properties>\n"
+                            f"{indent}  </profile>\n"
+                            f"{indent}</profiles>\n"
+                        )
+                        new_lines.insert(i, profile_block)
+                        break
+
     with open(file_path, 'w') as f:
         # Clean up double empty lines potentially introduced by pruning
         content = "".join(new_lines)
diff --git a/monorepo-migration/transform_workflow.py b/monorepo-migration/transform_workflow.py
index fba791634ebe..af8aa743aa08 100644
--- a/monorepo-migration/transform_workflow.py
+++ b/monorepo-migration/transform_workflow.py
@@ -33,11 +33,34 @@ def transform(content, lib_name):
           library:
             - '{lib_name}/**'"""
 
+    clirr_template = f"""  clirr:
+    needs: filter
+    if: ${{{{ needs.filter.outputs.library == 'true' }}}}
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-java@v4
+      with:
+        distribution: temurin
+        java-version: 11
+    - run: java -version
+    - run: .kokoro/build.sh
+      env:
+        JOB_TYPE: clirr
+        BUILD_SUBDIR: {lib_name}"""
+
     in_jobs = False
     skip_current_job = False
     current_job_is_windows = False
+    current_job_is_lint = False
+    
+    skip_lines_count = 0
     
     for line in lines:
+        if skip_lines_count > 0:
+            skip_lines_count -= 1
+            continue
+
         if line.startswith('name:') and not in_jobs:
             name_match = re.match(r'^name:\s*(.*)', line)
             if name_match:
@@ -62,11 +85,12 @@ def transform(content, lib_name):
             if job_match:
                 job_name = job_match.group(1)
                 current_job_is_windows = False # Reset for new job
+                current_job_is_lint = (job_name == 'lint')
+                skip_current_job = False
                 if job_name == 'clirr':
                     skip_current_job = True
+                    new_lines.extend(clirr_template.splitlines())
                     continue
-                else:
-                    skip_current_job = False
                 
                 if job_name != 'filter':
                     new_lines.append(line)
@@ -84,10 +108,29 @@ def transform(content, lib_name):
                 new_lines.append("      run: git config --system core.longpaths true")
                 continue
 
+            if 'name: Support longpaths' in line and current_job_is_windows:
+                skip_lines_count = 1
+                continue
+
+            if '- uses: actions/checkout' in line and current_job_is_lint:
+                new_lines.append("    - uses: actions/checkout@v4")
+                new_lines.append("      with:")
+                new_lines.append("        fetch-depth: 0")
+                continue
+
+            if 'JOB_TYPE: lint' in line and current_job_is_lint:
+                new_lines.append(line)
+                new_lines.append("        HEAD_SHA: ${{ github.event.pull_request.head.sha }}")
+                new_lines.append("        BASE_SHA: ${{ github.event.pull_request.base.sha }}")
+                continue
+
             if 'run: echo "SUREFIRE_JVM_OPT=' in line and '!java17' not in line:
                 line = line.replace('" >> $GITHUB_ENV', ' -P !java17" >> $GITHUB_ENV')
             if 'build.bat' in line:
                 line = line.replace('build.bat', 'build.sh')
+            if '.kokoro/conformance.sh' in line:
+                short_name = lib_name.replace('java-', '')
+                line = line.replace('.kokoro/conformance.sh', f'.kokoro/{short_name}-conformance.sh')
 
             new_lines.append(line)
     return "\n".join(new_lines)
diff --git a/monorepo-migration/update_changes_filters.py b/monorepo-migration/update_changes_filters.py
new file mode 100644
index 000000000000..5b00c0bde8cd
--- /dev/null
+++ b/monorepo-migration/update_changes_filters.py
@@ -0,0 +1,43 @@
+#!/usr/bin/env python3
+# Copyright 2026 Google LLC
+#
+# 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 sys
+
+def update_changes_filters(ci_yaml, lib_name):
+    with open(ci_yaml, 'r') as f:
+        content = f.read()
+        
+    target = '  split-units:'
+    new_filter = f'''          {lib_name}:
+            - '{lib_name}/**'
+            - 'google-auth-library-java/**/*.java'
+            - 'google-auth-library-java/**/pom.xml'
+            - 'sdk-platform-java/**/*.java'
+            - 'sdk-platform-java/java-shared-dependencies/**/pom.xml'
+            - 'sdk-platform-java/gapic-generator-java-pom-parent/pom.xml'
+'''
+    if new_filter not in content:
+        content = content.replace(target, new_filter + target)
+        with open(ci_yaml, 'w') as f:
+            f.write(content)
+        print(f"Successfully added {lib_name} to changes job in {ci_yaml}.")
+    else:
+        print(f"{lib_name} is already configured in {ci_yaml}.")
+
+if __name__ == '__main__':
+    if len(sys.argv) != 3:
+        print(f"Usage: {sys.argv[0]} <ci_yaml> <lib_name>")
+        sys.exit(1)
+    update_changes_filters(sys.argv[1], sys.argv[2])
diff --git a/monorepo-migration/update_ci_filters.py b/monorepo-migration/update_ci_filters.py
new file mode 100644
index 000000000000..2a9704cdf838
--- /dev/null
+++ b/monorepo-migration/update_ci_filters.py
@@ -0,0 +1,42 @@
+#!/usr/bin/env python3
+# Copyright 2026 Google LLC
+#
+# 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 sys
+import re
+
+def update_ci_filters(ci_yaml, lib_name):
+    with open(ci_yaml, 'r') as f:
+        content = f.read()
+        
+    # match `!(...)` pattern in ci.yaml
+    pattern = r'!\(([^)]+)\)'
+    
+    def repl(match):
+        modules = match.group(1).split('|')
+        if lib_name not in modules:
+            modules.append(lib_name)
+            modules.sort()
+        return '!(' + '|'.join(modules) + ')'
+        
+    new_content = re.sub(pattern, repl, content)
+    with open(ci_yaml, 'w') as f:
+        f.write(new_content)
+    print(f"Successfully added {lib_name} to CI exclusions in {ci_yaml}.")
+
+if __name__ == '__main__':
+    if len(sys.argv) != 3:
+        print(f"Usage: {sys.argv[0]} <ci_yaml> <lib_name>")
+        sys.exit(1)
+    update_ci_filters(sys.argv[1], sys.argv[2])
diff --git a/monorepo-migration/update_generation_config.py b/monorepo-migration/update_generation_config.py
index 1ba7e6fc8c3e..2ab0c49f4b57 100644
--- a/monorepo-migration/update_generation_config.py
+++ b/monorepo-migration/update_generation_config.py
@@ -15,87 +15,40 @@
 
 import sys
 import yaml
-import re
 
-def get_library_id(lib):
-    """
-    Returns a unique identifier for a library.
-    Prefer 'library_name', then 'api_shortname'.
-    """
-    if 'library_name' in lib:
-        return f"java-{lib['library_name']}"
-    if 'api_shortname' in lib:
-        return f"java-{lib['api_shortname']}"
-    return "unknown"
-
-def merge_libraries(target_libs, source_libs):
+def update_config(target_path, source_path):
     """
-    Merges source_libs into target_libs.
-    Libraries are matched by get_library_id.
-    GAPICs are merged and deduplicated by proto_path.
-    The final list is sorted by library_id.
+    Appends the library configuration from the source_path to the target_path.
+    This avoids rewriting the entire target YAML, preserving all comments and ordering.
     """
-    # Map from library_id to library dict
-    target_map = {get_library_id(lib): lib for lib in target_libs}
-
-    for s_lib in source_libs:
-        lib_id = get_library_id(s_lib)
-        
-        # Clean up source library (remove repo fields)
-        s_lib_cleaned = {k: v for k, v in s_lib.items() if k not in ('repo', 'repo_short')}
-        
-        if lib_id in target_map:
-            t_lib = target_map[lib_id]
-            # Merge GAPICs
-            t_gapics_list = t_lib.get('GAPICs', [])
-            s_gapics_list = s_lib_cleaned.get('GAPICs', [])
-            
-            # Map by proto_path for deduplication
-            proto_map = {g['proto_path']: g for g in t_gapics_list}
-            for g in s_gapics_list:
-                proto_map[g['proto_path']] = g
-            
-            # Sort GAPICs by proto_path
-            sorted_protos = sorted(proto_map.keys())
-            t_lib['GAPICs'] = [proto_map[p] for p in sorted_protos]
-            
-            # Update other fields from source
-            for k, v in s_lib_cleaned.items():
-                if k != 'GAPICs':
-                    t_lib[k] = v
-        else:
-            target_map[lib_id] = s_lib_cleaned
-
-    # Return sorted list of libraries
-    sorted_ids = sorted(target_map.keys())
-    return [target_map[lib_id] for lib_id in sorted_ids]
-
-def update_config(target_path, source_path):
-    with open(target_path, 'r') as f:
-        target_content = f.read()
-    
     with open(source_path, 'r') as f:
         source_data = yaml.safe_load(f) or {}
 
-    # Load target data
-    target_data = yaml.safe_load(target_content) or {}
-    
-    target_libs = target_data.get('libraries', [])
     source_libs = source_data.get('libraries', [])
-    
-    merged_libs = merge_libraries(target_libs, source_libs)
-    target_data['libraries'] = merged_libs
+    if not source_libs:
+        print("No libraries found in source config.")
+        return
 
-    # Write back
-    with open(target_path, 'w') as f:
-        # Check if there was a license header in the original file
-        header_match = re.search(r'^(#.*?\n\n)', target_content, re.DOTALL)
-        if header_match:
-            f.write(header_match.group(1))
-        
-        # Use yaml.dump to write the data.
-        # sort_keys=False to preserve order of fields within libraries if possible (YAML 1.2+ usually does, but pyyaml depends)
-        yaml.dump(target_data, f, sort_keys=False, default_flow_style=False, indent=2)
+    # In standalone repos, there is usually only one library definition.
+    new_libs = []
+    for s_lib in source_libs:
+        # Clean up source library (remove repo fields as they are now internal to monorepo)
+        if 'repo' in s_lib:
+            del s_lib['repo']
+        if 'repo_short' in s_lib:
+            del s_lib['repo_short']
+        new_libs.append(s_lib)
+
+    # Dump the new library entries as a YAML string
+    # sort_keys=False preserves the field ordering (e.g., api_shortname first)
+    new_yaml_str = yaml.dump(new_libs, sort_keys=False, default_flow_style=False, indent=2)
+
+    # Append to the existing monorepo generation_config.yaml
+    # This ensures we don't rewrite the file and lose comments/ordering.
+    with open(target_path, 'a') as f:
+        f.write(new_yaml_str.rstrip() + "\n")
+
+    print(f"Appended {len(new_libs)} libraries to {target_path}")
 
 if __name__ == "__main__":
     if len(sys.argv) != 3:
diff --git a/monorepo-migration/update_linter_exclusions.py b/monorepo-migration/update_linter_exclusions.py
new file mode 100644
index 000000000000..e0cad10b1c39
--- /dev/null
+++ b/monorepo-migration/update_linter_exclusions.py
@@ -0,0 +1,37 @@
+#!/usr/bin/env python3
+# Copyright 2026 Google LLC
+#
+# 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 sys
+
+def update_linter(file_path, lib_name):
+    with open(file_path, 'r') as f:
+        content = f.read()
+    
+    target = '      [[ "${pomFile}" =~ .*java-vertexai.* ]] || \\'
+    replacement = f'      [[ "${{pomFile}}" =~ .*{lib_name}.* ]] || \\\n{target}'
+    
+    if target in content:
+        content = content.replace(target, replacement)
+        with open(file_path, 'w') as f:
+            f.write(content)
+        print(f"Successfully added {lib_name} to linter exclusions.")
+    else:
+        print(f"Target not found in {file_path}")
+
+if __name__ == '__main__':
+    if len(sys.argv) != 3:
+        print(f"Usage: {sys.argv[0]} file_path lib_name")
+        sys.exit(1)
+    update_linter(sys.argv[1], sys.argv[2])
diff --git a/monorepo-migration/update_root_pom.py b/monorepo-migration/update_root_pom.py
index fec12930dee3..dd1203ae28a0 100644
--- a/monorepo-migration/update_root_pom.py
+++ b/monorepo-migration/update_root_pom.py
@@ -14,6 +14,7 @@
 # limitations under the License.
 
 import sys
+import re
 
 def update_root_pom(pom_path, module_name):
     new_module = f'    <module>{module_name}</module>\n'
@@ -39,7 +40,7 @@ def update_root_pom(pom_path, module_name):
         java_lines = lines[start_java:end_java]
         if not any(f'<module>{module_name}</module>' in l for l in java_lines):
             java_lines.append(new_module)
-            java_lines.sort()
+            java_lines.sort(key=lambda line: m.group(1) if '<module>' in line and (m := re.search(r'<module>(.*?)</module>', line)) else line)
             lines = lines[:start_java] + java_lines + lines[end_java:]
     else:
         if not any(f'<module>{module_name}</module>' in l for l in lines):
diff --git a/monorepo-migration/update_samples_build.py b/monorepo-migration/update_samples_build.py
new file mode 100755
index 000000000000..50b837c055a4
--- /dev/null
+++ b/monorepo-migration/update_samples_build.py
@@ -0,0 +1,56 @@
+#!/usr/bin/env python3
+# Copyright 2026 Google LLC
+#
+# 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 sys
+import re
+
+def main():
+    if len(sys.argv) < 3:
+        print("Usage: update_samples_build.py <path_to_yaml> <library_name>")
+        sys.exit(1)
+        
+    file_path = sys.argv[1]
+    library_name = sys.argv[2]
+    
+    with open(file_path, 'r') as f:
+        content = f.read()
+        
+    if 'BUILD_SUBDIR=' in content:
+        print(f"BUILD_SUBDIR already present in {file_path}. Skipping.")
+        sys.exit(0)
+        
+    # Find the 'env:' line and insert 'BUILD_SUBDIR' after it
+    lines = content.splitlines()
+    new_lines = []
+    modified = False
+    
+    for line in lines:
+        new_lines.append(line)
+        match = re.match(r'^(\s*)env:\s*$', line)
+        if match and not modified:
+            indent = match.group(1)
+            # Insert BUILD_SUBDIR under env:
+            new_lines.append(f"{indent}- 'BUILD_SUBDIR={library_name}'")
+            modified = True
+            
+    if modified:
+        with open(file_path, 'w') as f:
+            f.write('\n'.join(new_lines) + '\n')
+        print(f"Successfully added BUILD_SUBDIR={library_name} to {file_path}")
+    else:
+        print(f"Warning: Could not find 'env:' block in {file_path}")
+
+if __name__ == '__main__':
+    main()