Add ShouldProcess support to mutating commands

[lipkau]

Summary

• Add ShouldProcess support to mutating configuration and server configuration commands
• Skip persistence when WhatIf declines mutation
• Add WhatIf regression coverage for add/set/remove command paths
• Keep module-qualified alias helpers active under WhatIf

Validation

• pwsh -NoLogo -NonInteractive -NoProfile -Command "Set-Location '/Users/LIO2MU/projects/AtlassianPS/agents/config-release-readiness/AtlassianPS.Configuration'; Invoke-Build -Task Build, Test"
• Tests Passed: 942, Failed: 0, Skipped: 19