Java Resolve Relative Path

The general way is to use the File class getCanonicalPath() method.
It's specifically documented to remove (resolve) the ../ and ./ that you're looking for.

Extracts from the docs:

This method first converts this pathname to absolute form if necessary [...] and then maps it to its unique form in a system-dependent way. This typically involves removing redundant names such as "." and ".." from the pathname, resolving symbolic links (on UNIX platforms), and converting drive letters to a standard case (on Microsoft Windows platforms).

Since you mentioned PHP, I'll assume a web context. With the Servlet API you can get a real path corresponding to a relative path using servletContext.getRealPath(relativePath)

Outside a web context you can use file.getAbsolutePath(), where file is java.io.File constructed with a relative path.