Read/write optimizations (#551)

Read/write optimizations (#551)

* Avoid one extra read call after the final bytes are read

If read returns less then the requested number of bytes, the file is at
EOF. This can be used in all places where a read is done, but it makes extra
impact in read_file where if the buffer is made one byte bigger than needed,
EOF can be detected before a unnecessary memory reallocation is done.

* Use write instead of fwrite to write the result file

This avoids the caching in stdio where a write is split into two (at least on
my system): first a small 4k one and then one with the remaining 60k.