Cleanup of files and incorporate Codacy analysis

[craigthomas]

This PR cleans up the source files and re-organizes them into better modules. It also does the following:

• README.md updated to point to correct uber-jar file for examples.
• Apache commons-cli removed and replaced with JCommander.
• Test files cleaned up.
• Explicit scopes inserted instead of relying on default package protection.
• Codacy issues addressed.

[codecov-io]

Codecov Report

Merging #7 into master will increase coverage by 3.06%.
The diff coverage is 42.85%.

@@             Coverage Diff              @@
##             master       #7      +/-   ##
============================================
+ Coverage     77.48%   80.55%   +3.06%     
  Complexity      199      199              
============================================
  Files            12       13       +1     
  Lines           875      833      -42     
  Branches         59       54       -5     
============================================
- Hits            678      671       -7     
+ Misses          191      155      -36     
- Partials          6        7       +1

Impacted Files	Coverage Δ	Complexity Δ
src/com/chip8java/emulator/runner/Arguments.java	0% <0%> (ø)	0 <0> (?)
src/com/chip8java/emulator/runner/Runner.java	0% <0%> (ø)	0 <0> (?)
src/com/chip8java/emulator/components/Screen.java	95.87% <100%> (ø)	19 <2> (?)
.../com/chip8java/emulator/components/ScreenMode.java	100% <100%> (ø)	5 <2> (?)
...java/emulator/listeners/TraceMenuItemListener.java	100% <100%> (ø)	3 <0> (ø)	⬇️
...ava/emulator/components/CentralProcessingUnit.java	93.66% <100%> (ø)	136 <0> (?)
src/com/chip8java/emulator/components/Memory.java	100% <100%> (ø)	10 <1> (?)
...mulator/listeners/ResetMenuItemActionListener.java	100% <100%> (ø)	2 <1> (ø)	⬇️
...8java/emulator/listeners/StepMenuItemListener.java	100% <100%> (ø)	3 <0> (ø)	⬇️
...rc/com/chip8java/emulator/components/Keyboard.java	42.1% <33.33%> (ø)	6 <2> (?)
... and 6 more

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