diff --git a/finalize_manifest.py b/finalize_manifest.py
index 3c023021..aa9a8393 100755
--- a/finalize_manifest.py
+++ b/finalize_manifest.py
@@ -35,11 +35,15 @@ def generate_trusted_files(root_dir, already_added_files):
                                 r'boot/.*'
                                 r'|\.dockerenv'
                                 r'|\.dockerinit'
-                                r'|etc/mtab'
                                 r'|dev/.*'
+                                r'|etc/gshadow.*'
+                                r'|etc/mtab'
+                                r'|etc/\.pwd\.lock'
                                 r'|etc/rc(\d|.)\.d/.*'
+                                r'|etc/security/.*'
+                                r'|etc/shadow.*'
                                 r'|gramine/python/.*'
-                                r'|finalize_manifest\.py'
+                                r'|gramine/app_files/finalize_manifest\.py'
                                 r'|proc/.*'
                                 r'|sys/.*'
                                 r'|var/.*)$')
@@ -82,7 +86,7 @@ def generate_trusted_files(root_dir, already_added_files):
 
 def generate_library_paths():
     encoding = sys.stdout.encoding if sys.stdout.encoding is not None else 'UTF-8'
-    ld_paths = subprocess.check_output('ldconfig -v', stderr=subprocess.PIPE, shell=True)
+    ld_paths = subprocess.check_output('ldconfig -v -N -X', stderr=subprocess.PIPE, shell=True)
     ld_paths = ld_paths.decode(encoding).splitlines()
 
     # Library paths start without whitespace (in contrast to libraries found under this path)
@@ -107,7 +111,7 @@ def main(args=None):
     env = jinja2.Environment(loader=jinja2.FileSystemLoader('/'))
     env.globals.update({'library_paths': generate_library_paths(), 'env_path': os.getenv('PATH')})
 
-    manifest = '/entrypoint.manifest'
+    manifest = '/gramine/app_files/entrypoint.manifest'
     rendered_manifest = env.get_template(manifest).render()
     rendered_manifest_dict = toml.loads(rendered_manifest)
     already_added_files = extract_files_from_user_manifest(rendered_manifest_dict)
diff --git a/gsc.py b/gsc.py
index 4d51ce34..c48a9760 100755
--- a/gsc.py
+++ b/gsc.py
@@ -124,6 +124,12 @@ def extract_build_args(args):
                 sys.exit(1)
     return buildargs_dict
 
+def extract_user_from_image_config(config, env):
+    user = config['User']
+    if not user:
+        user = 'root'
+    env.globals.update({'app_user': user})
+
 def merge_two_dicts(dict1, dict2, path=[]):
     for key in dict2:
         if key in dict1:
@@ -167,6 +173,7 @@ def gsc_build(args):
     env.globals.update(yaml.safe_load(args.config_file))
     env.globals.update(vars(args))
     env.globals.update({'app_image': original_image_name})
+    extract_user_from_image_config(original_image.attrs['Config'], env)
     extract_binary_cmd_from_image_config(original_image.attrs['Config'], env)
     extract_working_dir_from_image_config(original_image.attrs['Config'], env)
 
@@ -383,11 +390,14 @@ def gsc_info_image(args):
 
     # Create temporary directory on the host for sigstruct file
     with tempfile.TemporaryDirectory() as tmpdirname:
+        # Grant owner, group and everyone else read-write-execute permissions on temporary dir, so
+        # that even non-root users in Docker images can copy `entrypoint.sig` into it
+        os.chmod(tmpdirname,0o777)
         # Copy sigstruct file from Docker container into temporary directory on the host
         docker_socket.containers.run(args.image,
-                                 '\'cp entrypoint.sig /tmp/host/ 2>/dev/null || :\'',
-                                 entrypoint=['sh', '-c'], remove=True,
-                                 volumes={tmpdirname: {'bind': '/tmp/host', 'mode': 'rw'}})
+            '\'cp /gramine/app_files/entrypoint.sig /tmp/host/ 2>/dev/null || :\'',
+            entrypoint=['sh', '-c'], remove=True,
+            volumes={tmpdirname: {'bind': '/tmp/host', 'mode': 'rw'}})
         sigstruct = {}
         with open(os.path.join(tmpdirname, "entrypoint.sig"), 'rb') as sig:
             attr = read_sigstruct(sig.read())
diff --git a/templates/Dockerfile.common.build.template b/templates/Dockerfile.common.build.template
index 54e4b5c0..14647c5c 100644
--- a/templates/Dockerfile.common.build.template
+++ b/templates/Dockerfile.common.build.template
@@ -8,9 +8,21 @@ FROM gsc-{{Gramine.Image}} AS gramine
 # Combine Gramine image with the original app image
 FROM {{app_image}}
 
+# Temporarily switch to the root user to install packages
+USER root
+
 # Install distro-specific packages to run Gramine (e.g., python3, protobuf, toml, etc.)
 {% block install %}{% endblock %}
 
+# Create a directory that will store apploader.sh and entrypoint files.
+RUN mkdir -p /gramine/app_files
+
+# Make the app image user owner of /gramine/app_files directory
+RUN chown {{app_user}} /gramine/app_files/
+
+# Switch back to original app_image user
+USER {{app_user}}
+
 # Copy path-specific installation of Gramine
 {% if debug %}
 COPY --from=gramine /gramine/ /gramine/
@@ -19,28 +31,28 @@ COPY --from=gramine /gramine/meson_build_output /gramine/meson_build_output
 {% endif %}
 
 # Copy helper scripts and Gramine manifest
-COPY *.py /
-COPY apploader.sh /
-COPY entrypoint.manifest /
+COPY --chown={{app_user}} *.py /gramine/app_files/
+COPY --chown={{app_user}} apploader.sh /gramine/app_files/
+COPY --chown={{app_user}} entrypoint.manifest /gramine/app_files/
 
 # Generate trusted arguments if required
 {% if not insecure_args %}
 RUN /gramine/meson_build_output/bin/gramine-argv-serializer \
-        {{binary}} {{binary_arguments}} "{{"\" \"".join(cmd)}}" > /trusted_argv
+        {{binary}} {{binary_arguments}} "{{"\" \"".join(cmd)}}" > /gramine/app_files/trusted_argv
 {% endif %}
 
 # Docker entrypoint/cmd typically contains only the basename of the executable so create a symlink
-RUN cd / \
+RUN cd /gramine/app_files/ \
     && which {{binary}} | xargs ln -s || true
 
 # Include Meson build output directory in $PATH
 ENV PATH="/gramine/meson_build_output/bin:$PATH"
 
 # Mark apploader.sh executable, finalize manifest, and remove intermediate scripts
-RUN chmod u+x /apploader.sh \
-    && /usr/bin/python3 -B /finalize_manifest.py \
-    && rm -f /finalize_manifest.py
+RUN chmod u+x /gramine/app_files/apploader.sh \
+    && /usr/bin/python3 -B /gramine/app_files/finalize_manifest.py \
+    && rm -f /gramine/app_files/finalize_manifest.py
 
 # Define default command
-ENTRYPOINT ["/bin/bash", "/apploader.sh"]
+ENTRYPOINT ["/bin/bash", "/gramine/app_files/apploader.sh"]
 CMD [{% if insecure_args %} "{{'", "'.join(cmd)}}" {% endif %}]
diff --git a/templates/Dockerfile.common.sign.template b/templates/Dockerfile.common.sign.template
index 606ecef3..8040a35c 100644
--- a/templates/Dockerfile.common.sign.template
+++ b/templates/Dockerfile.common.sign.template
@@ -1,15 +1,15 @@
 # Sign image in a separate stage to ensure that signing key is never part of the final image
 FROM {{image}} as unsigned_image
 
-COPY gsc-signer-key.pem /gsc-signer-key.pem
+COPY gsc-signer-key.pem /gramine/app_files/gsc-signer-key.pem
 
 RUN {% block path %}{% endblock %} gramine-sgx-sign \
-      --key /gsc-signer-key.pem \
-      --manifest /entrypoint.manifest \
-      --output /entrypoint.manifest.sgx
+      --key /gramine/app_files/gsc-signer-key.pem \
+      --manifest /gramine/app_files/entrypoint.manifest \
+      --output /gramine/app_files/entrypoint.manifest.sgx
 
 # This trick removes all temporary files from the previous commands (including gsc-signer-key.pem)
 FROM {{image}}
 
-COPY --from=unsigned_image /*.sig /
-COPY --from=unsigned_image /*.sgx /
+COPY --from=unsigned_image /gramine/app_files/*.sig /gramine/app_files/
+COPY --from=unsigned_image /gramine/app_files/*.sgx /gramine/app_files/
diff --git a/templates/apploader.common.template b/templates/apploader.common.template
index ccc0e410..48c852a4 100644
--- a/templates/apploader.common.template
+++ b/templates/apploader.common.template
@@ -11,8 +11,10 @@ set -e
 # Default to Linux-SGX if no PAL was specified
 if [ -z "$GSC_PAL" ] || [ "$GSC_PAL" == "Linux-SGX" ]
 then
-    gramine-sgx-get-token --quiet --sig /entrypoint.sig --output /entrypoint.token
-    gramine-sgx /entrypoint {% if insecure_args %}{{binary_arguments}} "${@}"{% endif %}
+    gramine-sgx-get-token --quiet \
+        --sig /gramine/app_files/entrypoint.sig --output /gramine/app_files/entrypoint.token
+    gramine-sgx /gramine/app_files/entrypoint \
+        {% if insecure_args %}{{binary_arguments}} "${@}"{% endif %}
 else
-    gramine-direct /entrypoint {{binary_arguments}} "${@}"
+    gramine-direct /gramine/app_files/entrypoint {{binary_arguments}} "${@}"
 fi
diff --git a/templates/entrypoint.common.manifest.template b/templates/entrypoint.common.manifest.template
index 20f2902e..5fbc8c37 100644
--- a/templates/entrypoint.common.manifest.template
+++ b/templates/entrypoint.common.manifest.template
@@ -1,4 +1,4 @@
-libos.entrypoint = "/{{binary}}"
+libos.entrypoint = "/gramine/app_files/{{binary}}"
 
 # Add distro-specific `loader.entrypoint` and `loader.env.LD_LIBRARY_PATH`
 {% block loader %}{% endblock %}
@@ -22,9 +22,9 @@ sgx.debug = {% if debug %} true {% else %} false {% endif %}
 loader.argv0_override = "{{binary}}"
 loader.insecure__use_cmdline_argv = true
 {% else %}
-loader.argv_src_file = "file:/trusted_argv"
+loader.argv_src_file = "file:/gramine/app_files/trusted_argv"
 sgx.trusted_files = [
-  "file:/trusted_argv",
+  "file:/gramine/app_files/trusted_argv",
 ]
 {% endif %}
 
diff --git a/test/generic.manifest b/test/generic.manifest
index 0700527c..71891da4 100644
--- a/test/generic.manifest
+++ b/test/generic.manifest
@@ -5,5 +5,5 @@ sgx.enclave_size = "4G"
 sgx.thread_num = 8
 
 sgx.trusted_files = [
-  "file:/entrypoint.manifest",  # unused entry, only to test merging of manifests
+  "file:/gramine/app_files/entrypoint.manifest",  # unused entry, only to test merging of manifests
 ]