Fix issue with old libgit2 API calls causing the PHP extension to not load on compilation

Upon attempting to compile and utilise the PHP module, we were getting repeated:

```
PHP Warning:  PHP Startup: Unable to load dynamic library
'/usr/lib/php/modules/git2.so' - /usr/lib/php/modules/git2.so: undefined
symbol: git_index_get in Unknown on line 0
```

Errors on Apache restart, seems the index.c file for the extension was attempting to utilise API calls that have been renamed in the libgit2 library.

This change fixes this and loads the extension, and through our usage scenarios so far works as intended.

This commit fixes issues #44 and #28