diff --git a/docker/ci-runner/Dockerfile b/docker/ci-runner/Dockerfile
index a734451a11533307c67551452655bf6951d7235d..b35811a7d841a445e034ae812a2ee16bd55eae56 100644
--- a/docker/ci-runner/Dockerfile
+++ b/docker/ci-runner/Dockerfile
@@ -1,4 +1,6 @@
-FROM python:3.12
+# This dockerfile is used throughout steps of the CI/CD pipeline
+# It contains dependencies to execute the template and run tests
+FROM python:3.13
 
 RUN python -m pip install --upgrade pip
 RUN python -m pip install --upgrade cookiecutter tox twine
diff --git a/{{cookiecutter.project_slug}}/.gitlab-ci.yml b/{{cookiecutter.project_slug}}/.gitlab-ci.yml
index b4e3610be0cd53f508c1915a5d45989564a1cbdb..e7d1fe0677279eea6b46645d39d40325292dbf45 100644
--- a/{{cookiecutter.project_slug}}/.gitlab-ci.yml
+++ b/{{cookiecutter.project_slug}}/.gitlab-ci.yml
@@ -2,8 +2,6 @@ default:
   image:
     name: $CI_REGISTRY_IMAGE/ci-build-runner:$CI_COMMIT_REF_SLUG
     pull_policy: always
-  before_script:
-    - python --version # For debugging
   cache:
     paths:
       - .cache/pip
@@ -24,12 +22,13 @@ stages:
 variables:
   PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
 
+# Job templates from Gitlab that scan for security issues or leaked secrets
 include:
   - template: Security/SAST.gitlab-ci.yml
   - template: Security/Dependency-Scanning.gitlab-ci.yml
   - template: Security/Secret-Detection.gitlab-ci.yml
 
-# Prepare image to run ci on
+# Prepare image to run ci on, image will be used in most jobs
 trigger_prepare:
   stage: prepare
   trigger:
@@ -53,16 +52,6 @@ sast:
       pmd-apex, security-code-scan, sobelow, spotbugs
   stage: test
 
-dependency_scanning:
-  # override default before_script, job won't have Python available
-  before_script:
-    - uname
-
-secret_detection:
-  # override default before_script, job won't have Python available
-  before_script:
-    - uname
-
 # Basic setup for all Python versions for which we don't have a base image
 .run_unit_test_version_base:
   before_script:
@@ -71,6 +60,7 @@ secret_detection:
     - python -m pip install --upgrade tox twine
 
 # Run all unit tests for Python versions except the base image
+# The base image is used for the highest Python version
 run_unit_tests:
   extends: .run_unit_test_version_base
   stage: test
@@ -95,6 +85,7 @@ run_unit_tests_coverage:
     paths:
       - htmlcov/*
 
+# Build and packge the project
 package_files:
   stage: package
   artifacts:
@@ -104,6 +95,7 @@ package_files:
   script:
     - tox -e build
 
+# Build the sphinx documentation
 package_docs:
   stage: package
   artifacts:
@@ -113,6 +105,7 @@ package_docs:
   script:
     - tox -e docs
 
+# Build a tiny docker image that contains the minimal dependencies to run this project
 docker_build:
   stage: images
   image: docker:latest
@@ -203,6 +196,7 @@ publish_to_readthedocs:
     - echo "scp docs/* ???"
     - exit 1
 
+# automatically create a release on Gitlab for every tagged commit
 release_job:
   stage: publish
   image: registry.gitlab.com/gitlab-org/release-cli:latest
diff --git a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
index ce46e6463265d2ad9704a24ae7f467cb7b50d8d9..c7c1b720cfc8d8d631b4c7c2640aebd0499b3a08 100644
--- a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
+++ b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
@@ -1,3 +1,7 @@
+# run several checks prior to creating a commit or pushing to a remote
+# These can be skipped (but you shouldn't generally as the pipeline will fail)
+# using `git push / commit --no-check`
+# for more information see: https://pre-commit.com/
 default_stages: [ pre-commit, pre-push ]
 default_language_version:
   python: python3
diff --git a/{{cookiecutter.project_slug}}/README.md b/{{cookiecutter.project_slug}}/README.md
index 25f215207307771b9fefe5658653fe4816828721..612d22ac310c3e272dcfca9efed19c5a45be3c7a 100644
--- a/{{cookiecutter.project_slug}}/README.md
+++ b/{{cookiecutter.project_slug}}/README.md
@@ -57,5 +57,7 @@ To automatically apply most suggested linting changes execute:
 
 ```tox -e format```
 
+The configuration for linting and tox can be found in `pyproject.toml`
+
 ## License
 This project is licensed under the Apache License Version 2.0
diff --git a/{{cookiecutter.project_slug}}/bin/install-hooks/pre-commit.sh b/{{cookiecutter.project_slug}}/bin/install-hooks/pre-commit.sh
deleted file mode 100755
index 792a3aabef83dc4ebf0c94635ae1de0e7412c479..0000000000000000000000000000000000000000
--- a/{{cookiecutter.project_slug}}/bin/install-hooks/pre-commit.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash
-
-if [ ! -f "setup.sh" ]; then
-  echo "pre-commit.sh must be executed with repository root as working directory!"
-  exit 1
-fi
-
-pre-commit install --hook-type pre-push
diff --git a/{{cookiecutter.project_slug}}/docker/ci-runner/Dockerfile b/{{cookiecutter.project_slug}}/docker/ci-runner/Dockerfile
index 6063354805d6e2e35534ee5d09f80b51f856495b..5b45f3a8d8701901238be5c0b5509656b4b3c41f 100644
--- a/{{cookiecutter.project_slug}}/docker/ci-runner/Dockerfile
+++ b/{{cookiecutter.project_slug}}/docker/ci-runner/Dockerfile
@@ -1,3 +1,5 @@
+# This dockerfile is used throughout steps of the CI/CD pipeline
+# It contains dependencies to run tests
 FROM python:3.13
 
 RUN python -m pip install --upgrade pip
diff --git a/{{cookiecutter.project_slug}}/docker/{{cookiecutter.project_slug}}/Dockerfile b/{{cookiecutter.project_slug}}/docker/{{cookiecutter.project_slug}}/Dockerfile
index 1f7eb275020d13ed45cb7b0983949c12161ff953..e4f7edbedddadf9b39ff8192eda9c372fbe91e48 100644
--- a/{{cookiecutter.project_slug}}/docker/{{cookiecutter.project_slug}}/Dockerfile
+++ b/{{cookiecutter.project_slug}}/docker/{{cookiecutter.project_slug}}/Dockerfile
@@ -1,18 +1,28 @@
+# This dockerfile creates a minimal docker image that can run the project.
+# It can copy the result of `tox -e build` from the host to the container
+# or build from source inside the container.
+# Set `docker build --build-arg BUILD_ENV=copy` to copy from the host, rebuild otherwise
+# contrarily, to the ci image it does not contain any dependencies used for testing.
 ARG BUILD_ENV=no_copy
 
+# Build without copying from host inside docker
 FROM python:3.13 AS build_no_copy
 ADD ../../requirements.txt .
 COPY ../.. /work
-RUN rm -r /work/dist | true
+RUN rm -rf /work/dist
 RUN python -m pip install --user tox
 WORKDIR /work
 RUN python -m tox -e build
 
+# Copy build package from host `dist` directory
 FROM python:3.13 AS build_copy
 COPY dist /work/dist
 
+# Dynamically set `build` from `build_no_copy` or `build_copy` depending on
+# `BUILD_ENV` argument
 FROM build_${BUILD_ENV} AS build
 
+# Copy build stage files into final python slim image and install
 FROM python:3.13-slim
 COPY --from=build /work/dist /dist
 RUN python -m pip install /dist/*.whl
diff --git a/{{cookiecutter.project_slug}}/docs/cleanup.py b/{{cookiecutter.project_slug}}/docs/cleanup.py
index 3a4508d859234544bea35b1008e3c8e4f73d7cc0..c88889067f1dc736a881d565ee02460f8cd05148 100644
--- a/{{cookiecutter.project_slug}}/docs/cleanup.py
+++ b/{{cookiecutter.project_slug}}/docs/cleanup.py
@@ -3,6 +3,16 @@
 #  Copyright (C) 2023 ASTRON (Netherlands Institute for Radio Astronomy)
 #  SPDX-License-Identifier: Apache-2.0
 
+"""
+Remove generated source documentation files except for index.rst
+
+If a source file is created, documentation is generated and the source file is later
+removed. The documentation for this source file will persists.
+
+This file ensures generated source documentation files, which are automatically
+generated from source, are removed between every build.
+"""
+
 import os
 
 file_dir = os.path.dirname(os.path.realpath(__file__))
@@ -15,7 +25,7 @@ if not os.path.exists(clean_dir):
 
 for file_name in os.listdir(clean_dir):
     file = os.path.join(clean_dir, file_name)
-    
+
     if file_name == "index.rst":
         continue
 
diff --git a/{{cookiecutter.project_slug}}/setup.sh b/{{cookiecutter.project_slug}}/setup.sh
index 4548910b6ba00d9f564aea2ac5ddfab50c1d77db..6939c0502f2f95e42566748ce507829eb2190785 100755
--- a/{{cookiecutter.project_slug}}/setup.sh
+++ b/{{cookiecutter.project_slug}}/setup.sh
@@ -4,8 +4,10 @@
 # SPDX-License-Identifier: Apache-2.0
 #
 
-# This file's directory is used to determine the station control directory
-# location.
+# Substitute BASH_SOURCE if unset this is required for simple shells
+# such as the one found in docker or alpine docker images.
+# `#! /usr/bin/env bash` does not actually ensure the sourcing is executed
+# using BASH
 if [ -z ${BASH_SOURCE} ]; then
   BASH_SOURCE=${(%):-%x}
 fi
@@ -24,7 +26,7 @@ source "$VENV_DIR/bin/activate"
 python -m pip install pre-commit
 python -m pip install "tox>=4.21.0"
 
-# Install git pre-commit pre-push hook
-if [ ! -f "${ABSOLUTE_PATH}/.git/hooks/pre-push.legacy" ]; then
-  source "${ABSOLUTE_PATH}/bin/install-hooks/pre-commit.sh"
+# Install git pre-commit pre-push hook if not already installed
+if [ ! -f "${ABSOLUTE_PATH}/.git/hooks/pre-push" ]; then
+  pre-commit install --hook-type pre-push
 fi