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* Handle destination directories more gracefully
* The storage.output_dir is now the storage.root to avoid generating a sub-directory beneath the temporary working directory
* The destination directory is created, then resolved by realpath to avoid generating the destination directory within the temporary working directory when a relative path is used as input
* Replace the original file instead of using rename()
* rename() cannot operate across file system boundaries
* Dynamically allocate rootdirs array
* Use realpath on positional arguments
* Convert all markdown files to HTML
* README.html files are considered entry points and are linked as index.html
* Assign retcode after indexing
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