Add more comments and tidy up

Dockerfile

@@ -1,8 +1,11 @@
 # syntax=docker/dockerfile:1
 
+# Build the all stages of the image
 # docker build -t chaste .
-# docker build --target base -t chaste/base .  # Alternative: build base image
-# docker run -it --rm -v chaste_data:/home/chaste chaste
+# Alternative: build base image only
+# docker build --target base -t chaste/base .
+# Run the image (with a named volume and process management enabled)
+# docker run -it --init --rm -v chaste_data:/home/chaste chaste
 
 ARG BASE=oracular
 FROM ubuntu:${BASE} AS base
@@ -130,9 +133,6 @@ RUN python -m venv --upgrade-deps "${CHASTE_BUILD_DIR}/texttest_venv" && \
 # Create Chaste src, build, output and projects folders
 RUN mkdir -p "${CHASTE_SOURCE_DIR}" "${CHASTE_BUILD_DIR}" "${CHASTE_TEST_OUTPUT}" && \
     ln -s "${CHASTE_PROJECTS_DIR}" projects
-# DEPRECATED: Transitionary symlinks for build and output directories
-# RUN ln -s "${CHASTE_BUILD_DIR}" lib && \
-#     ln -s "${CHASTE_TEST_OUTPUT}" testoutput
 
 # Fix git permissions issue CVE-2022-24765
 RUN git config --global --add safe.directory "${CHASTE_SOURCE_DIR}"