Fix incorrect usage of InputStream.read(byte[]) through code

[lfcnassif]

Follow up of #1452, we can replace all of them by the safer InputStream.readNBytes() method.

[lfcnassif]

One last curiosity about this: InputStream.read(byte[]) or InputStream.read(byte[], int off, int len) are expected to read at least 1 byte if end of stream is NOT reached (I thought it could return 0 in some situations). InputStream.skip(N) can return 0 even if N > 0 and if end of stream is NOT reached.