Fix confusing param display and added an alert when running module main steps

[catmandx]

Before, when passing module parameters that differs from the default one, the app wrongly displays that the default value is being used: for example param "enableDnsBruteFocing" in "fast" routine

❯ osmedeus.exe -f fast -t example.com -p "enableDnsBruteFocing=true" 
...
[2024-02-15T17:19:19]  INFO 🔘 Toggleable and Skippable Parameters that being use: enablePermutation=false, enableDnsBruteFocing=false,
...

Change the order when parsing parameters so that user-supplied parameters values overwrites default values. After:

❯ osmedeus.exe -f fast -t example.com -p "enableDnsBruteFocing=true" 
...
[2024-02-15T17:19:19]  INFO 🔘 Toggleable and Skippable Parameters that being use: enablePermutation=false, enableDnsBruteFocing=true,
...

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When the main module steps takes too long, it could be confusing when users only see "Running prepare scripts for module xxx" for a very long time, so I've added a message when the main steps run.

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Fixed 2 typos.