File upload

- added LINE_SIZE variable in FileEntity to count number of bytes in
each sequence
- for resumed uploads, skip buffered reader to the last sequence line
- added rewriteBatchedStatements in conn config

Outstanding issues:
- while looping and saving sequences, the FileEntity instance keeps an
arraylist of all added sequences, causing an out of memory exception.
should this arraylist be populated in the first place or cleared with
every commit?
- file uploading is still too slow, i wonder if rewriteBatchedStatements
is actually working...
- nested commit operation within flush operation
-