partial update to rarefy_even_depth

This will add the expected behavior of "jack-knife" subsampling without
replacement. Currently, the subsampling includes replacement (and is
probably much faster and memory efficient).
v1.5.20 added sampling without replacement in rarefy_even_depth

Still needs unit tests for the new behavior. The default behavior is
the same. Needs testing/check before merging with master branch.
v1.5.20 further revisions and unit tests for rarefy_even_depth

More robust, more obvious what is going on with the RNG seed, etc.
There are now some unit tests for the the new `replace=FALSE` option.
v1.5.20 added first version of read_tree_greengenes

-This fixes an issue with greengenes annotated newick format for their
public release trees.
- This version is not finished. As-is, `read_tree_greengenes` would not
pass unit tests, because it's doing something weird with the OTU
labels, even though it is reading the newick file without an error
(unlike `read.tree`).
- Need to identify where the node/tip-mangling is coming from.
v1.5.20 `read_tree_greengenes` now working, unit tests, etc.

Also some doc updates for better seealso links.
v1.5.20 Fix bug in `tax_glom` when highest taxonomic rank specified

This solves Issue 223
https://github.com/joey711/phyloseq/issues/223
Merge pull request #228 from joey711/update-rarefy

v1.5.20 Bugfixes, `read_tree_greengenes`, and a `replace` optional parameter to rarefy_even_depth()