Add support for user-defined SVG colors for cell types in PhysiCell settings

[drbergman]

No description provided.

[Copilot]

Pull request overview

This PR adds a configuration-driven way to override SVG cell coloring by cell type name in PhysiCell settings, while keeping automatic palette assignment (and extending it beyond the original fixed palette size).

Changes:

• Introduces <cell_colors><cell_color name="...">...</cell_color></cell_colors> parsing under <SVG> into PhysiCell_Settings.
• Updates paint_by_number_cell_coloring() to (a) honor user-specified colors, (b) skip user-claimed palette colors, and (c) generate additional colors via golden-angle HSV spacing.
• Adds commented XML documentation blocks describing the new setting across multiple sample/unit-test configs.

Reviewed changes

Copilot reviewed 37 out of 37 changed files in this pull request and generated 16 comments.

Show a summary per file

File	Description
modules/PhysiCell_settings.h	Adds state to store whether SVG cell colors were specified and the name→color map.
modules/PhysiCell_settings.cpp	Parses <cell_colors> under <SVG> into settings.
modules/PhysiCell_pathology.h	Adds includes needed for new SVG color validation / processing helpers.
modules/PhysiCell_pathology.cpp	Validates user-provided colors, assigns per-cell-type colors (palette + HSV generation), and uses them in SVG output.
config/PhysiCell_settings.xml	Adds a commented example/documentation block for the new <cell_colors> option.
sample_projects/immune_function/config/PhysiCell_settings.xml	Adds a commented example/documentation block for the new <cell_colors> option.
sample_projects_intracellular/boolean/physiboss_cell_lines/config/PhysiCell_settings.xml	Adds a commented example/documentation block for the new <cell_colors> option.
unit_tests/custom_DCs_2substrates/config/PhysiCell_settings.xml	Adds a commented example/documentation block for the new <cell_colors> option.
sample_projects_physipkpd/template_pkpd/config/pkpd_model.xml	Adds a commented example/documentation block for the new <cell_colors> option.
sample_projects_physipkpd/moa_proliferation/config/pkpd_model.xml	Adds a commented example/documentation block for the new <cell_colors> option.
sample_projects_physipkpd/moa_necrosis/config/pkpd_model.xml	Adds a commented example/documentation block for the new <cell_colors> option.
sample_projects_physipkpd/moa_motility/config/pkpd_model.xml	Adds a commented example/documentation block for the new <cell_colors> option.
sample_projects_physipkpd/moa_apoptosis/config/pkpd_model.xml	Adds a commented example/documentation block for the new <cell_colors> option.
sample_projects_physipkpd/confluence_start-deprecated/config/pkpd_model.xml	Adds a commented example/documentation block for the new <cell_colors> option.
sample_projects_physipkpd/combo/config/pkpd_model.xml	Adds a commented example/documentation block for the new <cell_colors> option.

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