Fix/file size limit

Removes a limit on the file size of Cached and Indexed MzML files by using std::streampos consistently throughout the code. Specifically, using int to store file offsets turned out to be a bad idea since this can only address files up to 2 GB.

- also contains code to read a std::streampos type from an XML (e.g. used for indexed MzML)
- fixes some xerces resource leaks
- adds more error checks