Refactored function names in R/cleanup.R

[teddyCodex]

Description

Refactored specified function names in R/cleanup.R based on issue #7

Original	Modified	User Facing
clean_string	cleanString	✅
string2accnum	extractAccNum	✅
make_accnums_unique	ensureUniqAccNum	✅
cleanup_fasta_header	cleanFAHeaders	✅
remove_empty	removeEmptyRows	✅
repeat2s	condenseRepeatedDomains	✅
replaceQMs	replaceQuestionMarks	✅
remove_astrk	removeAsterisks	✅
remove_tails	removeTails	✅
cleanup_species	cleanSpecies	✅
cleanup_clust	cleanClusters	✅
cleanup_domarch	cleanDomainArchitecture	✅
cleanup_gencontext	cleanGenomicContext	✅
cleanup_GeneDesc	cleanGeneDescription	✅
pick_longer_duplicate	selectLongestDuplicate	✅
cleanup_lineage	cleanLineage	✅

Fixes issue #38

What kind of change(s) are included?

• Feature (adds or updates new capabilities)
• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (these changes would cause existing functionality to not work as expected).

Checklist

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• I have read and followed the CONTRIBUTING.md guidelines.
• I have searched for existing content to ensure this is not a duplicate.
• I have performed a self-review of these additions (including spelling, grammar, and related).
• I have added comments to my code to help provide understanding.
• I have added a test which covers the code changes found within this PR.
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[teddyCodex]

@jananiravi @the-mayer
File containing other occurrences of the functions.

function_occurrences #38.txt

[the-mayer]

Resolved NAMESPACE conflict, updated cleanString() refs. Merging!