diff --git a/infra/base-images/base-builder/indexer/manifest_types.py b/infra/base-images/base-builder/indexer/manifest_types.py
index bb4239c695be..664d4dc01ee5 100644
--- a/infra/base-images/base-builder/indexer/manifest_types.py
+++ b/infra/base-images/base-builder/indexer/manifest_types.py
@@ -38,6 +38,7 @@
 import urllib.request
 
 import manifest_constants
+
 import pathlib
 
 SRC_DIR = manifest_constants.SRC_DIR
@@ -433,7 +434,7 @@ def save_build(
 
     with tempfile.NamedTemporaryFile() as tmp:
       mode = "w:gz" if archive_path.suffix.endswith("gz") else "w"
-      with tarfile.open(tmp.name, mode) as tar:
+      with tarfile.open(tmp.name, mode, dereference=True) as tar:
 
         def _save_dir(
             path: pathlib.PurePath,
diff --git a/projects/calcite-avatica/Base64Fuzzer.java b/projects/calcite-avatica/Base64Fuzzer.java
deleted file mode 100644
index 2f2cb51ed540..000000000000
--- a/projects/calcite-avatica/Base64Fuzzer.java
+++ /dev/null
@@ -1,36 +0,0 @@
-// Copyright 2023 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 com.code_intelligence.jazzer.api.FuzzedDataProvider;
-import java.io.IOException;
-import org.apache.calcite.avatica.util.Base64;
-
-// Generated with https://github.com/ossf/fuzz-introspector/tree/main/tools/auto-fuzz
-// Minor modifications to beautify code and ensure exception is caught.
-// Heuristic name: jvm-autofuzz-heuristics-1
-// Target method: [org.apache.calcite.avatica.util.Base64] public static java.lang.String encodeBytes(byte[],int) throws java.io.IOException
-public class Base64Fuzzer {
-  public static void fuzzerTestOneInput(FuzzedDataProvider data) {
-    try {
-      if (data.consumeBoolean()) {
-        Base64.encodeBytes(data.consumeRemainingAsBytes());
-      } else {
-        Base64.decode(data.consumeRemainingAsBytes());
-      }
-    } catch (IOException | IllegalArgumentException e) {
-      // Known exception
-    }
-  }
-}
diff --git a/projects/calcite-avatica/ConnectStringParserFuzzer.java b/projects/calcite-avatica/ConnectStringParserFuzzer.java
deleted file mode 100644
index 282c6d3c9ddd..000000000000
--- a/projects/calcite-avatica/ConnectStringParserFuzzer.java
+++ /dev/null
@@ -1,33 +0,0 @@
-// Copyright 2023 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 com.code_intelligence.jazzer.api.FuzzedDataProvider;
-import java.sql.SQLException;
-import java.util.Properties;
-import org.apache.calcite.avatica.ConnectStringParser;
-
-// Generated with https://github.com/ossf/fuzz-introspector/tree/main/tools/auto-fuzz
-// Minor modifications to beautify code and ensure exception is caught.
-// Heuristic name: jvm-autofuzz-heuristics-1
-// Target method: [org.apache.calcite.avatica.ConnectStringParser] public static java.util.Properties parse(java.lang.String) throws java.sql.SQLException
-public class ConnectStringParserFuzzer {
-  public static void fuzzerTestOneInput(FuzzedDataProvider data) {
-    try {
-      ConnectStringParser.parse(data.consumeRemainingAsString());
-    } catch (SQLException e) {
-      // Known exception
-    }
-  }
-}
diff --git a/projects/calcite-avatica/Dockerfile b/projects/calcite-avatica/Dockerfile
index cd492ad27b49..880b47070ef5 100644
--- a/projects/calcite-avatica/Dockerfile
+++ b/projects/calcite-avatica/Dockerfile
@@ -15,5 +15,5 @@
 ##########################################################################
 FROM gcr.io/oss-fuzz-base/base-builder-jvm
 RUN git clone --depth 1 https://github.com/apache/calcite-avatica calcite-avatica
-COPY *.sh *.java $SRC/
+COPY *.sh $SRC/
 WORKDIR $SRC/calcite-avatica
diff --git a/projects/calcite-avatica/build.sh b/projects/calcite-avatica/build.sh
index aa4d8ad499a2..17cc52e0266e 100644
--- a/projects/calcite-avatica/build.sh
+++ b/projects/calcite-avatica/build.sh
@@ -15,31 +15,40 @@
 #
 ##########################################################################
 
-# Gradle build with gradle wrapper
+# Clean up caches
 rm -rf $HOME/.gradle/caches/
-./gradlew clean build shadowJar -x test
+
+# Build project and copy dependencies
+./gradlew clean :core:jar :core:testClasses :core:copyFuzzDependencies -x test
 ./gradlew --stop
 
+# Find version
 CURRENT_VERSION=$(./gradlew properties | grep ^version: | cut -d" " -f2)
-cp "./shaded/core/build/libs/avatica-$CURRENT_VERSION-shadow.jar" $OUT/avatica.jar
-ALL_JARS="avatica.jar"
 
-# The classpath at build-time includes the project jars in $OUT as well as the
-# Jazzer API.
-BUILD_CLASSPATH=$(echo $ALL_JARS | xargs printf -- "$OUT/%s:"):$JAZZER_API_PATH
+# Copy jars to $OUT
+cp core/build/fuzz-dependencies/*.jar $OUT/
+cp core/build/libs/avatica-core-$CURRENT_VERSION.jar $OUT/avatica-core.jar
+cp metrics/build/libs/avatica-metrics-$CURRENT_VERSION.jar $OUT/avatica-metrics.jar
+
+# Copy fuzzer classes to $OUT (preserving package structure)
+cp -r core/build/classes/java/test/* $OUT/
+
+# Create a consolidated list of all jars for the classpath
+ALL_JARS=$(find $OUT -maxdepth 1 -name "*.jar" | xargs -n1 basename)
 
-# All .jar and .class files lie in the same directory as the fuzzer at runtime.
+# The runtime classpath will include all jars in $OUT and the this_dir itself for classes
 RUNTIME_CLASSPATH=$(echo $ALL_JARS | xargs printf -- "\$this_dir/%s:"):\$this_dir
 
-for fuzzer in $(find $SRC -maxdepth 1 -name '*Fuzzer.java')
-do
-  fuzzer_basename=$(basename -s .java $fuzzer)
-  javac -cp $BUILD_CLASSPATH $fuzzer
-  cp $SRC/$fuzzer_basename.class $OUT/
+# Dynamically find all fuzzer classes in the specified package
+FUZZER_CLASSES_DIR="$OUT/org/apache/calcite/avatica/fuzz"
+FUZZERS=$(find "$FUZZER_CLASSES_DIR" -maxdepth 1 -name "*Fuzzer.class" -exec basename {} .class \;)
 
-  # Create an execution wrapper that executes Jazzer with the correct arguments.
+# For each fuzzer, create a wrapper script
+for fuzzer_basename in $FUZZERS
+do
+  target_class="org.apache.calcite.avatica.fuzz.$fuzzer_basename"
+  
   echo "#!/bin/bash
-
   # LLVMFuzzerTestOneInput for fuzzer detection.
   this_dir=\$(dirname "\$0")
   if [[ "\$@" =~ (^| )-runs=[0-9]+($| ) ]]
@@ -49,13 +58,13 @@ do
     mem_settings='-Xmx2048m:-Xss1024k'
   fi
 
-  LD_LIBRARY_PATH="$JVM_LD_LIBRARY_PATH":\$this_dir \
+  LD_LIBRARY_PATH=\"$JVM_LD_LIBRARY_PATH\":\$this_dir \
     \$this_dir/jazzer_driver                        \
     --agent_path=\$this_dir/jazzer_agent_deploy.jar \
     --cp=$RUNTIME_CLASSPATH                         \
-    --target_class=$fuzzer_basename                 \
-    --jvm_args="\$mem_settings"                     \
+    --target_class=$target_class                 \
+    --jvm_args=\"\$mem_settings\"                     \
     \$@" > $OUT/$fuzzer_basename
 
-    chmod u+x $OUT/$fuzzer_basename
+  chmod u+x $OUT/$fuzzer_basename
 done
diff --git a/projects/geos/Dockerfile b/projects/geos/Dockerfile
index 735e0afd3495..a009ab7e87c2 100644
--- a/projects/geos/Dockerfile
+++ b/projects/geos/Dockerfile
@@ -17,6 +17,6 @@
 FROM gcr.io/oss-fuzz-base/base-builder
 RUN apt-get update && apt-get install -y cmake
 # fallback to github if main git server is not responding
-RUN git clone --depth 1 https://git.osgeo.org/gitea/geos/geos.git || git clone --depth 1 https://github.com/libgeos/geos.git
+RUN git clone --depth 1 https://gitea.osgeo.org/geos/geos || git clone --depth 1 https://github.com/libgeos/geos.git
 COPY run_tests.sh build.sh $SRC/
 WORKDIR $SRC/geos
diff --git a/projects/geos/project.yaml b/projects/geos/project.yaml
index 940f0c93eff9..739388aca0c2 100644
--- a/projects/geos/project.yaml
+++ b/projects/geos/project.yaml
@@ -9,7 +9,7 @@ auto_ccs :
 sanitizers:
 - address
 - undefined
-main_repo: 'https://git.osgeo.org/gitea/geos/geos.git'
+main_repo: "https://gitea.osgeo.org/geos/geos"
 
 fuzzing_engines:
   - afl
diff --git a/projects/poppler/project.yaml b/projects/poppler/project.yaml
index 0e752a504283..66d7e8da827c 100644
--- a/projects/poppler/project.yaml
+++ b/projects/poppler/project.yaml
@@ -12,7 +12,7 @@ fuzzing_engines:
 auto_ccs:
   - jonathan@titanous.com
   - adam.reichold@t-online.de
-main_repo: 'https://anongit.freedesktop.org/git/poppler/poppler.git'
+main_repo: "https://gitlab.freedesktop.org/poppler/poppler"
 fuzzing_engines:
  - afl
  - honggfuzz
diff --git a/projects/postgis/Dockerfile b/projects/postgis/Dockerfile
index 824a76075ce9..69bdf947215d 100644
--- a/projects/postgis/Dockerfile
+++ b/projects/postgis/Dockerfile
@@ -16,7 +16,7 @@
 
 FROM gcr.io/oss-fuzz-base/base-builder:ubuntu-24-04
 
-RUN git clone --depth 1 https://git.osgeo.org/gitea/postgis/postgis.git postgis
+RUN git clone --depth 1 https://gitea.osgeo.org/postgis/postgis postgis
 WORKDIR postgis
 RUN bash ./fuzzers/install_oss_fuzz_build_deps.sh
 RUN apt-get update && \
diff --git a/projects/postgis/project.yaml b/projects/postgis/project.yaml
index a345e12c55df..686801bc0ce1 100644
--- a/projects/postgis/project.yaml
+++ b/projects/postgis/project.yaml
@@ -6,7 +6,7 @@ auto_ccs:
   - "even.rouault@gmail.com"
   - "pramsey@cleverelephant.ca"
   - "komzpa@gmail.com"
-main_repo: 'https://git.osgeo.org/gitea/postgis/postgis.git'
+main_repo: "https://gitea.osgeo.org/postgis/postgis"
 
 fuzzing_engines:
   - afl
diff --git a/projects/python-markdownify/Dockerfile b/projects/python-markdownify/Dockerfile
index a924e07ebd5e..448c3aebbd34 100644
--- a/projects/python-markdownify/Dockerfile
+++ b/projects/python-markdownify/Dockerfile
@@ -15,6 +15,6 @@
 ##########################################################################
 FROM gcr.io/oss-fuzz-base/base-builder-python
 RUN pip3 install --upgrade pip
-RUN git clone http://github.com/matthewwithanm/python-markdownify python-markdownify
+RUN git clone https://github.com/matthewwithanm/python-markdownify python-markdownify
 COPY *.sh *py $SRC/
 WORKDIR $SRC/python-markdownify
diff --git a/projects/python-markdownify/project.yaml b/projects/python-markdownify/project.yaml
index de472f426174..5899fedaa390 100644
--- a/projects/python-markdownify/project.yaml
+++ b/projects/python-markdownify/project.yaml
@@ -1,5 +1,5 @@
-homepage: http://github.com/matthewwithanm/python-markdownify
-main_repo: http://github.com/matthewwithanm/python-markdownify
+homepage: https://github.com/matthewwithanm/python-markdownify
+main_repo: https://github.com/matthewwithanm/python-markdownify
 language: python
 fuzzing_engines:
 - libfuzzer