Update 'running commands with snakemake' section

[florence-bockting]

Fixes #39 and is related to #41.

Description

This PR suggests improvements for the Section 'Running commands with snakemake' by providing

• support for (new) users in creating and editing files in a command line interface (Add explicit shell commands for file system operations #41)
• explanations of snakemake options (showing long and short format, Explanation of options when introducing new commands #39)
• updating the Exercise (Challenge) for building on gained knowledge within lesson.

TODO

• check whether site builds locally via sandpaper::serve(), sandpaper::build_lesson(), and sandpaper::check_lesson()

[github-actions]

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Rendered Changes

🔍 Inspect the changes: https://github.com/carpentries-incubator/hpc-workflows/compare/md-outputs..md-outputs-PR-44

The following changes were observed in the rendered markdown documents:

 01-introduction.md | 100 ++++++++++++++++++++++++++++++++++++++++++++---------
 md5sum.txt         |   2 +-
 2 files changed, 84 insertions(+), 18 deletions(-)

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⏱️ Updated at 2026-05-31 11:22:27 +0000