Bug fixes for irods-php

This pull request contains two commits.

The first removes all closing PHP tags `?>` from .php files and ensures each file ends in an EOL character. Omitting the `?>` tag is widely required by PHP style guides, including Zend Framework 2 and PSR-1. Depending on the PHP interpreter, including closing tags in PHP only files can cause the program to exit on an error.
Files were ended with a newline (specifically a linefeed), because failing to end the last line of a file with a newline character can cause issues with some UNIX-based tools. All EOLs should have been converted to \n when the changes were pushed to GitHub, but it's possible that this is not the case.

The second commit modifies a loop in prods/src/RODSGenQueSelFlds.class.php to reduce the chance of array out of bounds errors.