Move exception classes into their respective subpackages/submodules

See CHANGELOG.md for a description of the changes. Fixes #577.
`FastqParseError` is only used in `parse_fastq`, which is a generator (doesn't deal with `SequenceCollection`s). I put `StockholmParseError` here because it's used in `StockholmAlignment`, though I think both of these will get shuffled around after `skbio.io` gets added.