Dockerfile optimizations and PHP updates

Optimized Dockerfile for readability and image-size;

- Combined `RUN` statements to reduce the number of layers produced
- Replaced `ADD` with `COPY` (add will be deprecated in future)
- Re-organized files to reduce the number of `COPY` commands required
and be more flexible
- Wrapped long lines for readability
- Cleared ‘apt-get’ cache to reduce image size

Although these are just quick optimizations, the resulting image was reduced from 681.2 MB to 598.2 MB

Updated PHP versions

- PHP 5.3.28 -> 5.3.29
- PHP 5.4.24 -> 5.4.32
- PHP 5.5.8 -> 5.5.16