diff --git a/.envtemplate b/.envtemplate
index 2265975..3b181c3 100644
--- a/.envtemplate
+++ b/.envtemplate
@@ -15,7 +15,6 @@ AUTOBIDS_DICOM_SERVER_STUDYINSTANCEUID_WILDCARD="" # Falsy
 AUTOBIDS_CFMM2TAR_PATH="/images/cfmm2tar.sif"
 AUTOBIDS_CFMM2TAR_BINDS="/home:/home,/tmp:/tmp"
 AUTOBIDS_CFMM2TAR_DOWNLOAD_DIR=""
-AUTOBIDS_CFMM2TAR_STORAGE_DIR=""
 AUTOBIDS_CFMM2TAR_TIMEOUT=100000
 AUTOBIDS_TAR2BIDS_PATH="/images/tar2bids.sif"
 AUTOBIDS_TAR2BIDS_BINDS="/home:/home,/tmp:/tmp"
@@ -35,7 +34,7 @@ AUTOBIDS_ARCHIVE_SSH_PORT=2222
 AUTOBIDS_ARCHIVE_SSH_KEY="~/.ssh/id_rsa.pub"
 AUTOBIDS_ARCHIVE_TIMEOUT=100000
 
-AUTOBIDS_DICOM_PI_BLACKLIST = []
+AUTOBIDS_DICOM_PI_BLACKLIST = [] 
 
 AUTOBIDS_HEURISTIC_GIT_URL="git@github.com:example/heuristics.git"
 AUTOBIDS_HEURISTIC_REPO_PATH=""
diff --git a/.pylintrc b/.pylintrc
deleted file mode 100644
index 6978bde..0000000
--- a/.pylintrc
+++ /dev/null
@@ -1,9 +0,0 @@
-[MASTER]
-# List of plugins (as comma separated values of python module names) to load,
-# usually to register additional checkers.
-load-plugins=pylint_flask,pylint_flask_sqlalchemy,pylint_pytest,pylint.extensions.comparetozero,pylint.extensions.redefined_variable_type,pylint.extensions.while_used,pylint.extensions.mccabe,pylint.extensions.typing,pylint.extensions.docstyle,pylint.extensions.private_import,pylint.extensions.broad_try_clause,pylint.extensions.comparison_placement,pylint.extensions.for_any_all,pylint.extensions.check_elif,pylint.extensions.docparams,pylint.extensions.empty_comment,pylint.extensions.code_style,pylint.extensions.eq_without_hash,pylint.extensions.overlapping_exceptions,pylint.extensions.redefined_loop_name,pylint.extensions.bad_builtin,pylint.extensions.no_self_use,pylint.extensions.set_membership,pylint.extensions.consider_ternary_expression,pylint.extensions.confusing_elif,pylint.extensions.emptystring
-generated-members=db.session.*,self.notifications.*,err.__cause__.*,app.logger, datalad.api.*
-ignored-classes=Tar2bidsRunForm,StudyConfigForm
-
-[SIMILARITIES]
-ignore-imports=yes
diff --git a/Dockerfile b/Dockerfile
index d99edb9..9db2e46 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -67,7 +67,6 @@ COPY --from=apptainer-builds /opt/apptainer-images /opt/apptainer-images/
 
 ENV OTHER_OPTIONS='--tls-aes'
 WORKDIR /opt/autobidsportal
-COPY ./entrypoint.sh /opt/autobidsportal/entrypoint.sh
 COPY ./autobidsportal.ini.example autobidsportal.ini
 COPY ./bids_form.py .
 
@@ -75,11 +74,10 @@ RUN git config --system user.name "Autobids Portal" \
     && git config --system user.email "autobids@dummy.com" \
     && WHEEL=$(ls /opt/wheels | grep whl) \
     && pip install --no-cache-dir "/opt/wheels/${WHEEL}[deploy]" \
-    && rm -r /opt/wheels \
-    && chmod +x /opt/autobidsportal/entrypoint.sh
+    && rm -r /opt/wheels 
 
 ENV DCM4CHE_VERSION=5.24.1
 ENV PATH=/apps/dcm4che/dcm4che-${DCM4CHE_VERSION}/bin:/apps/DicomRaw:/apps/cfmm2tar:/opt/apptainer/bin:$PATH
 ENV _JAVA_OPTIONS="-Xmx2048m"
 
-ENTRYPOINT ["/opt/autobidsportal/entrypoint.sh"]
+CMD ["uwsgi", "--ini=autobidsportal.ini"]
\ No newline at end of file
diff --git a/MANIFEST.in b/MANIFEST.in
deleted file mode 100644
index 0336b75..0000000
--- a/MANIFEST.in
+++ /dev/null
@@ -1,3 +0,0 @@
-recursive-include autobidsportal/templates *.html
-recursive-include autobidsportal/static *.css
-include autobidsportal/resources/bidsignore.default
diff --git a/compose.yaml b/compose.yaml
index a711124..6a98c13 100644
--- a/compose.yaml
+++ b/compose.yaml
@@ -11,7 +11,6 @@ services:
       AUTOBIDS_LOG_LEVEL: INFO
       AUTOBIDS_ROOT_URL: autobidsportal
       AUTOBIDS_CFMM2TAR_DOWNLOAD_DIR: /cfmm2tar-download
-      AUTOBIDS_CFMM2TAR_STORAGE_DIR: /tar-files
       AUTOBIDS_TAR2BIDS_DOWNLOAD_DIR: /datasets
       AUTOBIDS_TAR2BIDS_TEMP_DIR: /tmp
       AUTOBIDS_HEURISTIC_REPO_PATH: /home
@@ -37,10 +36,6 @@ services:
       AUTOBIDS_DICOM_SERVER_PASSWORD: "password"
       AUTOBIDS_DICOM_SERVER_TLS: "true"
       AUTOBIDS_DICOM_SERVER_STUDYINSTANCEUID_WILDCARD: "false"
-      AUTOBIDS_GITLAB_ACTIVE: "true"
-      AUTOBIDS_GITLAB_URL: "http://127.0.0.1:8080"
-      AUTOBIDS_GITLAB_TOKEN: "BFavxxb7gAodznnorhv7"
-      AUTOBIDS_GITHUB_ACTIVE: "false"
       GIT_AUTHOR_NAME: "Autobids Portal"
       GIT_AUTHOR_EMAIL: "autobids@example.com"
       GIT_COMMITER_NAME: "Autobids Portal"
diff --git a/entrypoint.sh b/entrypoint.sh
deleted file mode 100644
index 13bd99a..0000000
--- a/entrypoint.sh
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/bin/bash
-
-# Set to exit on error
-set -e
-
-# Functions
-ssh_known_hosts() {
-    # This causes problems if run as part of docker compose, but keeping this 
-    # in here as a hint for what to run
-    echo "Gathering public ssh keys of services..."
-    ssh-keyscan -p 2222 archive >> /etc/ssh/ssh_known_hosts
-    ssh-keyscan -p 2222 ria >> /etc/ssh/ssh_known_hosts
-    echo "Finished gathering keys."
-}
-
-
-flask_db() {
-    # Upgrade db task
-    echo "Upgrading flask database..."
-    flask db upgrade -d /usr/local/lib/python3.9/dist-packages/autobidsportal_migrations/
-    echo "Completed database upgrade."
-}
-
-
-init() {
-    # Init web app task
-    echo "+----------------------------+"
-    echo "| Starting autobidsportal... |"
-    echo "+----------------------------+"
-    uwsgi --ini=autobidsportal.ini
-}
-
-
-# Main body of code
-flask_db
-init
\ No newline at end of file