Add "dash" options to the bash scripts, and some additional refactoring#12

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mpaiao wants to merge 11 commits intomonanadmin:mainfrom

mpaiao:use_dash-options

Commits on Jan 5, 2026

Minor edits to the CD-CT scripts. The numbered scripts now use flags to specify which
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Commits on Jan 6, 2026

Added new options to the scripts for additional flexibility, and also to increase the
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Commits on Jan 8, 2026

1. Standardised the usage across all bash scripts to take in options (with dash) to avoid
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Function clean_tmp_files no longer exists. Remove option "-c" from all scripts.
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Replace hardcoded L55 with L${NLEV}. This is used for reporting an error only.
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Commits on Jan 10, 2026