Add MacOS build packaging tool

[OtabekRintaro]

This PR contains a tool for packaging MacOS build for FastSurfer and modified workflow to automate packaging on FastSurfer release.

build_release_package.sh script packages FastSurfer along with minimised freesurfer code.
Modified deploy.yml workflow builds and uploads packaged FastSurfers to artifacts on FastSurfer release.

• Folder structure change: Docker, Singularity and macos_build in the tools folder
• Static files used for installer customisation added into doc folder

[m-reuter]

python3.10 is hardcoded in a few places. We should try to make it easier to upgrade to a new python version in the future, which can happen pretty often. Maybe it is even possible to replace with python3 ?

[dkuegler]

Nice work, see comments.

[dkuegler]

We will also need to update the install instructions for macOS in doc/overview/INSTALL.md.

[dkuegler]

Lots of good stuff, some minor comments.

Big things:

1. Documentation of the new installation method (in doc/overview/INSTALL.md)
2. Fix the workflow
3. @dkuegler While the docker build seems to work, the docker "running" seems to have errors in the surface pipeline, I will have a look at that on Friday.

[dkuegler]

Looks good to me :)
Please change the PR from draft to ready to merge when you completed your testing.

[Copilot]

Pull Request Overview

This PR adds macOS build packaging tools for FastSurfer and reorganizes the project structure by moving Docker, Singularity, and build tools into a tools folder. The changes enable automated macOS package creation on release and improve project organization.

Key changes:

• New macOS packaging system with installer scripts and build tools
• Reorganized folder structure: Docker, Singularity, and build scripts moved to tools/ directory
• Added FreeSurfer configuration to pyproject.toml for centralized version management
• Updated documentation and workflows to reflect the new folder structure

Reviewed Changes

Copilot reviewed 34 out of 40 changed files in this pull request and generated 16 comments.

Show a summary per file

File	Description
tools/read_toml.py	New utility for extracting values from TOML configuration files
tools/macos_build/build_release_package.sh	Main script for building macOS installer packages
tools/macos_build/scripts/*.sh	Post-installation and FreeSurfer linking scripts for macOS
tools/build/install_fs_pruned.sh	Updated FreeSurfer installation script with improved download handling and pyproject.toml integration
pyproject.toml	Added FreeSurfer version and URL configuration
doc/overview/MACOS.md	New macOS-specific installation documentation
doc/overview/INSTALL.md	Updated installation instructions with macOS package option
.github/workflows/deploy.yml	Modified to build and upload macOS packages on release
tools/Docker/*	Moved Docker-related files from root to tools directory with path updates

Comments suppressed due to low confidence (2)

tools/build/install_fs_pruned.sh:68

• The embedded Python script (lines 52-68) for reading pyproject.toml is duplicated in multiple places in the codebase (also in tools/read_toml.py). Consider extracting this to a shared function or always using the dedicated tools/read_toml.py script to avoid code duplication and maintenance issues.
  tools/build/install_fs_pruned.sh:22
• Typo in usage message: "install_fs_prunded" should be "install_fs_pruned.sh"

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[OtabekRintaro]

doc build has failed due to cloudflare being down