Either install libhydrogen to a standard system location, or check out the source tree and build this extension directly against that.
Example building against libhydrogen sources:
$ mkdir src
$ cd src
$ git clone github.com/jedisct1/libhydrogen
$ git clone github.com/phplang/phydro
$ cd ohydro
$ phpize
$ ./configure --with-phydro=../libhydrogen
$ make