General maintenance, enhance editing options, and introduce additional processing variants including cortical areas

[kdiers]

This pull request introduces several updates and improvements across the codebase, focusing on bug fixes, documentation accuracy, new atlas support, enhanced editing options, and code simplification.

Atlas and Configuration Updates

• Added support for new ASHS atlas look-up tables (ashs-penn_abc_3t_t2_ent and ashs-penn_abc_3t_t2_ext) in get_atlases, including their label/index mappings and associated region lists.
• Added a new boundary label (bndba35) to the LUT dictionary for atlas configurations.

Enhance editing options

• Updated the default configuration options to include start_with_edited_labels and start_with_edited_masks in get_defaults.

Codebase Simplification and Cleanup

• Removed the unused newVtcsSgn variable and all related code from the getSeam and its subfunctions in computeCubeParam.py, simplifying the logic and return values.
• Removed commented-out and unused imports in computeCubeParam.py.

Documentation and Output Corrections

• Minor fixes.

[Copilot]

Pull request overview

This PR updates Hipsta’s atlas handling and processing pipeline to support additional Penn ABC-3T ASHS variants (including cortical areas), adds CLI options to resume processing from edited labels/masks, and performs general maintenance/cleanup (including additional debug/visualization outputs and minor documentation fixes).

Changes:

• Add two new built-in LUT variants (ashs-penn_abc_3t_t2_ent, ashs-penn_abc_3t_t2_ext) and related boundary label support.
• Introduce --start-with-edited-labels / --start-with-edited-masks to resume processing from edited outputs.
• Update cube parametrization / supplementary outputs (debug MGH outputs, seam logic simplification, additional orientation logic).

Reviewed changes

Copilot reviewed 14 out of 15 changed files in this pull request and generated 15 comments.

Show a summary per file

File	Description
VERSION	Bump version to 0.9.2-dev.
TUTORIAL.md	Fix automask argument descriptions and correct y-dimension table content.
pyproject.toml	Adjust Ruff lint configuration (global E501 ignore).
hipsta/utils/create_supplementary_files.py	Add boundary overlay support for ashs-penn_abc_3t_t2_ext and refine overlay creation gating.
hipsta/removeBoundaryMask.py	Add MGH output for boundary removal visualization.
hipsta/processLabels.py	Extend automask logic to handle new LUT variants / additional labels.
hipsta/hipsta.py	Add new --lut keywords and new resume-from-edited CLI flags; adjust pipeline flow accordingly.
hipsta/doc/documentation.py	Minor whitespace/docstring formatting.
hipsta/doc/DOCUMENTATION.md	Document new CLI flags and update supported segmentation text (partially).
hipsta/cutTetra.py	Minor numeric array construction cleanup.
hipsta/createTetraLabels.py	Conditionally create additional boundary masks and update output naming.
hipsta/computeCubeParam.py	Remove newVtcsSgn logic; add LUT-specific orientation handling and extra debug outputs.
hipsta/cfg/config.py	Add defaults for new resume flags.
hipsta/cfg/atlases.py	Add atlas variants and bndba35 label.
.github/workflows/build.yml	Update CI Python matrix.

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