standardize file copy to output

[drbergman]

Standardize how all files are copied to output. This serves several purposes:

• ensures that the config file is copied
  • previously handled in user-defined main.cpp
  • now done in core as we had been doing with rules, ic cells, and ic substrates
• optional default_basename argument in copy_file_to_output ensures standard file naming in output
  • ensures downstream tools can find the appropriate files, e.g. pcdl
  • does result in duplicate files in the output if the user-supplied name differs from the default base name, but this is minimal compared to the simulation data

Note: If a user retains the copy command in their main.cpp, this will just mean it is copied twice which will not cause errors.

[drbergman]

I have reviewed all the updated main.cpp's and they have all been properly updated. The episodes project has a unique structure, however, and is unchanged. Again, all this should mean is repeated copying for that project, but nothing excessive.

[Copilot]

Pull Request Overview

Standardize how configuration, microenvironment, geometry, and rule files are copied to the output directory by centralizing operations in copy_file_to_output with an optional default_basename parameter.

• Removed redundant manual cp commands from all sample project main.cpp files.
• Updated core utilities to accept a default_basename and invoke a second copy when needed.
• Applied copy_file_to_output uniformly in modules for settings, microenvironment, cell data, and rules.

Reviewed Changes

Copilot reviewed 27 out of 27 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
sample_projects/worm/main.cpp	Removed manual config copy
sample_projects/virus_macrophage/main.cpp	Removed manual config copy
sample_projects/template/main.cpp	Removed manual config copy
sample_projects/rules_sample/main.cpp	Removed manual config copy
sample_projects/pred_prey_farmer/main.cpp	Removed manual config copy
sample_projects/physimess/main.cpp	Removed manual config copy
sample_projects/mechano/main.cpp	Removed manual config copy
sample_projects/interactions/main.cpp	Removed manual config copy
sample_projects/immune_function/main.cpp	Removed manual config copy
sample_projects/heterogeneity/main.cpp	Removed manual config copy
sample_projects/custom_division/main.cpp	Removed manual config copy
sample_projects/cancer_immune/main-cancer_immune_3D.cpp	Removed manual config copy
sample_projects/cancer_biorobots/main.cpp	Removed manual config copy
sample_projects/biorobots/main.cpp	Removed manual config copy
sample_projects/asymmetric_division/main.cpp	Removed manual config copy
modules/PhysiCell_settings.cpp	Added default_basename arguments to copy settings XML
modules/PhysiCell_geometry.cpp	Added default_basename for cell CSV copy
core/PhysiCell_utilities.h	Extended copy_file_to_output signature with default
core/PhysiCell_utilities.cpp	Implemented double-copy logic with default_basename
core/PhysiCell_rules.cpp	Applied default_basename for rule file copy

Comments suppressed due to low confidence (2)

core/PhysiCell_utilities.cpp:383

• Using sprintf and system() with unvalidated filenames can lead to shell injection and portability issues; consider replacing this with std::filesystem::copy or another safe API.

sprintf(copy_command, "cp %s %s", filename.c_str(), output_filename.c_str());

core/PhysiCell_utilities.h:114

• Add unit tests for copy_file_to_output covering both the single-copy and double-copy (with non-empty default_basename) paths to verify correct behavior.

void copy_file_to_output(const std::string &filename, const std::string &default_basename = "");