Refactor Main, DSpot and Amplification

[andrewbwogi]

I've added some changes since #928. This would replace that PR.

[coveralls]

Pull Request Test Coverage Report for Build 2420

• 340 of 384 (88.54%) changed or added relevant lines in 15 files are covered.
• 7 unchanged lines in 3 files lost coverage.
• Overall coverage increased (+0.2%) to 84.031%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
dspot/src/main/java/eu/stamp_project/dspot/selector/PitMutantScoreSelector.java	0	1	0.0%
dspot/src/main/java/eu/stamp_project/utils/configuration/DSpotState.java	60	61	98.36%
dspot/src/main/java/eu/stamp_project/utils/DSpotUtils.java	0	2	0.0%
dspot/src/main/java/eu/stamp_project/utils/options/check/Checker.java	1	3	33.33%
dspot/src/main/java/eu/stamp_project/Main.java	6	11	54.55%
dspot/src/main/java/eu/stamp_project/utils/configuration/InitializeDSpot.java	99	115	86.09%
dspot/src/main/java/eu/stamp_project/utils/configuration/AmplificationSetup.java	78	95	82.11%

Files with Coverage Reduction	New Missed Lines	%
dspot/src/main/java/eu/stamp_project/utils/program/InputConfiguration.java	1	84.27%
dspot/src/main/java/eu/stamp_project/test_framework/AbstractTestFrameworkDecorator.java	3	28.57%
dspot/src/main/java/eu/stamp_project/test_framework/TestFramework.java	3	88.37%

Totals
Change from base Build 2419:	0.2%
Covered Lines:	4936
Relevant Lines:	5874

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💛 - Coveralls

[andrewbwogi]

This PR is ready for merge.

[danglotb]

Wonderful! Thank you.