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[#750] Use java.nio.file for file/path handling (#866)

String operations are used for the construction of file paths. Also,
many APIs in the codebase take in String arguments as file paths.

This method of file/path handling is error prone as creating paths using
string concatenation can lead to the creation of invalid paths.
Furthermore, checking if two paths resolve to the same file using string
equality is incorrect as it only tests if the strings are equal.

Let's refactor the codebase to use java.nio.file for file/path
handling as it provides a safe and platform-independent way to
perform operations on paths and properly separate the concerns of
parsing/stringifying paths and manipulating paths.

More information on why String operations are error-prone:
http://twistedoakstudios.com/blog/Post4872_dont-treat-paths-like-strings

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