First support for XStringSet interaction. Not testable yet.

Need to add the class union and phyloseq-class definitions, and also
the phyloseq constructor and merge_phyloseq, are among the most
important methods to add...
v1.3.20 update refseq=XStringSet alpha branch

Only conflict was in DESCRIPTION file. version number and biostrings
dependency version had to be manually updated, forward-looking to
actual merge/commit from this.
v1.3.20 incomplete support for refseq/XStringClass

Still need to update example data, include merge method for dealing
with XStringClass, and tests.
v1.3.20 Rebuilt example data with new class def
v1.3.20 Fixed issue w/ extract-method signature
v1.3.20 fix identical/equivalent issue in tests (again)
v1.3.20 bugfixes for phyloseq() constructor function

also added show-method for refseq slot.
v1.3.20 mod assignment methods to account for refseq
v1.3.20 revised some phyloseq infrastructure

Needs testing, more revisions to go.
prune_samples needs testing, further mod
- prune_* / reconcile_* / intersect_*
	- add intersect_samples() function, model after new version of
intersect_species()
	- rename intersect_species to intersect_taxa()
	- revise prune_samples, reuse intersect_samples
	- rm/replace reconcile_* functions with prune_*(intersect_*(), ps).
That's all it's doing now.
	- These changes make simpler / DRYer code. Easier to extend.
v1.3.20 Updated phyloseq infrastructure

- prune_* / reconcile_* / intersect_*
	- add intersect_samples() function, model after new version of
intersect_species()
	- rename intersect_species to intersect_taxa()
	- rm/replace reconcile_* functions with prune_*(intersect_*(), ps).
	- These changes make simpler / DRYer code. Easier to extend.
v1.3.20 add refseq import to import_qiime, import_biom

Still needs updated @usage
Needs tests
v1.3.20 added merge method for XStringSet, and lots of fixes

Still needs testing...
v1.3.20 added warn msg to merge_phyloseq_pair for XStringSet
v1.3.20 fixed minor bug in import_biom tree-reading section
v1.3.20 added ex/test files, tests, improve show method
v1.3.20 Support for reference sequences as XStringSet

- Final commit for v1.3.20
- fixes last issues with merge_taxa(), and adds further unit tests to
check logic, as well as informative error messages when merge_taxa()
goes wrong
- DRYer, better commented merge_taxa code
Merge pull request #177 from joey711/add-XStringSet

Support reference biological sequence for each OTU. This completes [Issue 127](https://github.com/joey711/phyloseq/issues/127)