Replace `alias` with `alias_method`

Done with `rubocop --auto-correct --only Alias`
Standardise on collection methods

Done with `rubocop --auto-correct --only CollectionMethods`
Replace deprecated File.exists? method

Done with `rubocop --auto-correct --only DeprecatedClassMethods`
Replace deprecated Hash methods

Done with `rubocop --auto-correct --only DeprecatedHashMethods`
Update rubocop todo list
Merge pull request #2953 from fog/style_method_names

Standardise method names based on style rules