Add flag for optional overwrite of pom files. Code refactor

[rnc]

Fixes #965

[codecov]

Codecov Report

Patch coverage: 86.36% and project coverage change: +0.03 🎉

Comparison is base (46a5d76) 83.81% compared to head (4803de1) 83.84%.

Additional details and impacted files

@@             Coverage Diff              @@
##               main     #970      +/-   ##
============================================
+ Coverage     83.81%   83.84%   +0.03%     
- Complexity     1947     1948       +1     
============================================
  Files           120      120              
  Lines          7187     7182       -5     
  Branches       1230     1228       -2     
============================================
- Hits           6024     6022       -2     
+ Misses          675      674       -1     
+ Partials        488      486       -2     

Impacted Files	Coverage Δ
...commonjava/maven/ext/core/ManipulationManager.java	88.88% <83.33%> (-0.31%)	⬇️
...mmonjava/maven/ext/manip/ManipulatingEventSpy.java	81.57% <100.00%> (+5.49%)	⬆️
...ain/java/org/commonjava/maven/ext/io/ConfigIO.java	72.34% <100.00%> (ø)
...c/main/java/org/commonjava/maven/ext/io/PomIO.java	90.30% <100.00%> (-0.18%)	⬇️

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