Various updates and changes to the documentation

[dkuegler]

This PR has various changes and updates to the fastsurfer documentation.

Two example:

• consistently mount/bind shared folders for singularity and docker in the same location as on the host file system (to simplify the documentation)
• move the singularity example into position 1 (instead of the docker example)

Todos:

• rebase the changes onto dev (currently on ClePol/CC_doc)
• review and test the documentation for consistency and completeness

[Copilot]

Pull request overview

This PR updates FastSurfer documentation to improve consistency and clarity. The main changes include:

• Standardizing mount/bind paths between Docker and Singularity to use the same locations as the host file system (using $HOME instead of mapping to different paths like /data, /output)
• Reordering examples to show Singularity first, then Docker
• Updating formatting and structure across documentation files

Changes:

• Unified path mounting approach: Docker and Singularity now mount folders to the same path inside containers as on the host
• Reordered examples: Singularity examples moved to position 1 throughout documentation
• Improved documentation structure with consistent headers and formatting

Reviewed changes

Copilot reviewed 34 out of 34 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
tools/Docker/README.md	Updated Docker examples to use $HOME paths consistently, fixed flag descriptions
doc/overview/SINGULARITY.md	Major restructuring with containerization explanation, updated examples
doc/overview/EXAMPLES.md	Swapped example order (Singularity first), updated paths to use $HOME
doc/overview/INSTALL.md	Updated references to example numbers after reordering
doc/scripts/RUN_FASTSURFER.md	Restructured flags documentation, added conditionally required section
recon_surf/README.md	Updated examples with consistent $HOME paths
README.md	Updated usage section with clearer flag explanations and $HOME paths
stools.sh	Minor comment typo fix
srun_fastsurfer.sh	Updated time limit warnings for CPU processing
Other files	Various formatting improvements, typo fixes, and structural updates

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[m-reuter]

Maybe try adding this:

numpydoc_validation_exclude = {
    r'\.WarmupCosineLR\.step$',  # Exclude only WarmupCosineLR.step
}

to conf.py and undo the "Ignore warning" commit.