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According to the hook_libraries_info() documentation:
/* * - path: (optional) A relative path from the directory of the library to the * actual library. Only required if the extracted download package contains * the actual library files in a sub-directory. */
Unfortunately, libraries_get_version() doesn't take this into account. This means that if you need to pull the version from the actual library file, you can't unless it's in the top level of the library path.
The attached patch updates libraries_get_version() to use the $library['path'] variable if set.