Wiki: Clarify installation instructions; add PETSc reconfigure section (#130)

I think it would be good to further expand and clarify the installation
instructions in the wiki:
- I added a section on how to reconfigure an existing PETSc
installation. I think this is useful since I assume that many users will
already have an existing installation
- I clearly separated the "local install" and "Docker" approaches and
their differences. I thought that it was slightly confusing in its
current state.
- I now explicitly state that the Docker image has everything
pre-installed and ready to use.
- I put the section on Docker at the very end, so that it is not
intertwined with the 'local installation' approach
- I simplified the 'Installing Mesh Adaptation modules' section with
various minor changes (will leave comments on specific changes)

---------

Co-authored-by: Joe Wallwork <22053413+jwallwork23@users.noreply.github.com>

Author: ddundo

wiki/Installation-Instructions.md

@@ -1,6 +1,8 @@
 The following installation instructions assume a Linux or Windows Subsystem for Linux (WSL) operating system.
-The mesh adaptation modules are dependent on a custom setup for Firedrake with PETSc from either a [local installation](#local-firedrake-installation) or a [pre-built Docker image](#installing-firedrake-via-docker-image).
-Once Firedrake is installed (or if you already have a working installation), see the section on [installing Animate, Goalie, or Movement](#installing-animate-goalie-or-movement).
+
+The mesh adaptation modules are dependent on a custom setup for Firedrake with PETSc, as described in the [local installation](#local-firedrake-installation) section below. Once Firedrake is installed, see the section on [installing Animate, Goalie, or Movement](#installing-animate-goalie-or-movement).
+
+Alternatively, you may use a [pre-built Docker image](#docker-container-approach) with Animate, Goalie, Movement, and all their dependencies preinstalled and ready to use.
 
 ## Local Firedrake installation
 
@@ -14,17 +16,53 @@ To use the mesh adaptation modules, we can install system dependencies (step 1)
 python3 ../firedrake-configure --show-petsc-configure-options | xargs -L1 ./configure --download-eigen --download-parmetis --download-mmg --download-parmmg
 ```
 
+### Reconfiguring an existing installation
+
+If you have previously installed PETSc without the additional mesh adaptation packages listed above, you can install them using PETSc's [reconfigure](https://petsc.org/release/install/multibuild/#reconfigure) script as follows:
+```
+cd $PETSC_DIR
+$PETSC_DIR/$PETSC_ARCH/lib/petsc/conf/reconfigure-$PETSC_ARCH.py --download-eigen --download-parmetis --download-mmg --download-parmmg
+make PETSC_DIR=${PETSC_DIR} PETSC_ARCH=${PETSC_ARCH} all
+```
+
+## Installing Mesh Adaptation modules
+
+The Mesh Adaptation packages Animate, Goalie, and Movement are installed as follows, denoting the package of interest by `<PACKAGE>`.
+First, ensure that you have activated the Python virtual environment associated with your Firedrake installation:
+```
+source /path/to/venv/bin/activate
+```
+
+Then clone the `<PACKAGE>` repository using [your preferred method](https://docs.github.com/en/get-started/git-basics/about-remote-repositories). For example, cloning with HTTPS URL is done as follows:
+```
+git clone https://github.com/mesh-adaptation/<PACKAGE>.git
+```
+
+Once cloned, the package can be [installed using pip](https://pip.pypa.io/en/stable/topics/local-project-installs/):
+```
+python3 -m pip install -e <PACKAGE>
+```
+
+## Updating
+
+It is highly recommended to keep your Firedrake installation and Mesh Adaptation software stack up to date.
+**We recommend updating the full stack at least once every two months.**
+
+* To update Firedrake and PETSc, follow the [official Firedrake instructions](https://www.firedrakeproject.org/install.html#updating-firedrake) on how to do so.
+* To update Animate/Goalie/Movement, simply change directory to where each one is located (`cd /path/to/package`) and run `git pull`.
+
 ## Docker container approach
 
-A bespoke Firedrake Docker image exists and can be downloaded and run as an alternative to the above:
+We provide a bespoke Docker image with PETSc, Firedrake, Animate, Goalie, and Movement already preinstalled.
+
+The image can be downloaded and run as follows:
 ```
 docker pull ghcr.io/mesh-adaptation/firedrake-parmmg:latest
 docker run -it ghcr.io/mesh-adaptation/firedrake-parmmg:latest
 ```
 
 For more information on how to run docker containers, see the [official documentation](https://docs.docker.com/engine/containers/run/). For example, since all data inside a container is only accessible from inside the container, it is useful to create [filesystem mounts](https://docs.docker.com/engine/containers/run/#filesystem-mounts) to be able to access data from outside the container.
 
-
 ### Using GPUs inside a container
 
 Passing the `--gpus` flag to `docker run` allows us to use GPUs inside containers (see [Docker documentation](https://docs.docker.com/reference/cli/docker/container/run/#gpus) for details). For example, to use all available GPUs, run the following:
@@ -51,36 +89,3 @@ Now you may proceed with installing GPU-supported software as normal. For exampl
 ```
 pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu126
 ```
-
-## Installing Mesh Adaptation modules
-
-The Mesh Adaptation packages can be installed through the following options, denoting the package of interest by `<PACKAGE>`.
-In both cases, make sure that you have activated the Python virtual environment that was created when you installed Firedrake.
-Ensure that you have activated the Python virtual environment associated with your Firedrake installation before following the steps below:
-```
-source /path/to/venv/bin/activate
-```
-
-### Cloning via HTTPS
-
-```
-git clone https://github.com/mesh-adaptation/<PACKAGE>.git
-cd <PACKAGE>
-make install
-```
-
-### Cloning via SSH
-
-```
-git@github.com:mesh-adaptation/<PACKAGE>.git
-cd <PACKAGE>
-make install
-```
-
-## Updating
-
-It is highly recommended to keep your Firedrake installation and Mesh Adaptation software stack up to date.
-**We recommend updating the full stack at least once every two months.**
-
-* To update Firedrake and PETSc, follow the [official Firedrake instructions](https://www.firedrakeproject.org/install.html#updating-firedrake) on how to do so.
-* To update Animate/Goalie/Movement, simply change directory to where each one is located (`cd /path/to/package`) and run `git pull`.