* Move core library sources into src/lib/core
* Move command-line programs into src/cli

* 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

* Now return an error code
* Completely rewrote replace_text()