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feat: #523 - Resolved node_module source files or directories are no longer returned from Project#getSourceFiles() and getDirectories()

BREAKING CHANGE: Source files implicitly resolved in the node_modules directory are no longer returned by `Project#getSourcesFiles()` and `getDirectories()`. Either add them to the project explicitly or navigate to them via methods like `.getSourceFile("node_modules/library/pathToFile.d.ts")` or `.getDirectory("node_modules")`.

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