New features, bug fixes and improved documentation

[tzschmidt]

• Add variable support to settings: define multiple settings at once
• Add instance dependent command line arguments
• Multiple bug fixes (gen options, instance paths, ...)
• Improve documentation

[Copilot]

Pull request overview

This pull request adds significant new functionality to the benchmarktool, including variable support for settings and instance-dependent command-line arguments. The changes refactor how command-line arguments are handled throughout the system, moving from simple strings to dictionaries with "pre" and "post" keys. Additionally, the PR renames the -f/--force option to -u/--update and adds a new -c/--clean option for better control over output directory management.

Changes:

• Add variable support to settings allowing automatic generation of multiple setting configurations from ranges or value pools
• Change command-line argument handling from strings to dictionaries with "pre" and "post" keys for system, setting, and instance levels
• Rename -f/--force to -u/--update and add -c/--clean for output directory management, plus improve documentation

Reviewed changes

Copilot reviewed 25 out of 25 changed files in this pull request and generated 14 comments.

Show a summary per file

File	Description
tests/test_entry.py	Update tests to reflect renamed command-line arguments (force → update/clean)
tests/runscript/test_runscript_parser.py	Update parser tests for new cmdline dict structure and variable support
tests/runscript/test_runscript_classes.py	Update class tests for cmdline dict structure and gen_scripts signature changes
tests/ref/test_template.sh	Update template to use new cmdline variables (sys_cmd, setting_cmd, inst_cmd)
tests/ref/test_bench/spec.xml	Add cmdline attributes to test spec
tests/ref/runscripts/test_runscript.xml	Add variable examples and cmdline attributes
src/benchmarktool/runscript/schemas/runscript.xsd	Add variable element schema and cmdline attributes
src/benchmarktool/runscript/schemas/benchmark_spec.xsd	Add cmdline attributes to instance and folder elements
src/benchmarktool/runscript/runscript.py	Refactor cmdline to dict, add cmdline support to instances/folders, update gen_scripts signature
src/benchmarktool/runscript/parser.py	Implement variable parsing logic with range and pool support
src/benchmarktool/entry_points.py	Update command-line argument parsing (force → update, add clean)
src/benchmarktool/init/templates/seq-generic.sh	Update template to use new cmdline variable references
src/benchmarktool/init/runscripts/runscript-example.xml	Add variable usage examples
src/benchmarktool/init/runscripts/runscript-all.xml	Add comprehensive examples of new features
src/benchmarktool/init/programs/clingo-latest	Add example wrapper script for clingo
mkdocs.yml	Add glossary to navigation (with typo)
docs/reference/index.md	Add glossary reference
docs/reference/glossary.md	Add new glossary documentation
docs/reference/encoding_support.md	Update example to use new cmdline variables
docs/getting_started/workflow/index.md	Expand documentation on SUT setup and exec usage
docs/getting_started/init/index.md	Add recommendation to run in new directory
docs/getting_started/index.md	Update runlim single option documentation
docs/getting_started/gen/templates.md	Document new cmdline variable references
docs/getting_started/gen/runscript.md	Add comprehensive variable and cmdline documentation
docs/getting_started/gen/index.md	Update gen command documentation

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[rkaminsk]

I skimmed over the docs and left some comments.

Regarding the glossary, I think that the descriptions for some items are not enough to be useful. It would probably be better to link back into the documentation for further descriptions and examples.