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[Feature] Adds --scope and --ignore support for bootstrap, exec, run,…
… clean and ls (#386) * Refactoring to allow scope and ignore flags to work accross with bootstrap, exec, run, clean and ls commands * fixed issue with bootstrapConfig and publishCOnfig ignore flags being ignored * Adds tests for --ignore and --scope flag behaviour in ls, exec, run, clean and bootstrap commands * Adds tests for PakcageUtilities.getFilteredPackages() * Linting: removed unused imports * fixes broken test in bootstrap due to non-normalized paths * fixes broken tests in BootstrapCommand from windowns symlinks * Removed the configFlags from PublishCommand * Updated readme with --scoped and --ignore flags information * fix(): Refactored Repository and PackageUtilities to remove filtering responsibility from Repository * Fixes broken test for LSCommand
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