Inline comments in parameters files now ignored.

Fixes #738.
fixes issue 773
replaced ``/home/qiime`` with ``$HOME``
all instances of ``/home/ubuntu/qiime_software`` are now ``$QIIME_DIR``
remaining instances of ``/home/qiime`` and ``/home/ubuntu`` are now
``$HOME``
the files in which ``$QIIME_DIR`` was added also have explicit exports
in place to define that environment variable
changed  to /Users/mcdonald
Merge pull request #935 from wasade/issue313

Issue313
Merge pull request #933 from jrrideout/issue-738

Inline comments in parameters files now ignored.
Merge pull request #934 from wasade/issue773

fixes issue #773
Multiple corrections to the docs

Fixed a few typos, broken-links, etc

Fixes #707, fixes #760 and fixes #724
Merge pull request #932 from jrrideout/issue-876

split_libraries.py disallows -s without -q.
Merge pull request #923 from justin212k/705

fixes #705
Merge pull request #936 from ElDeveloper/dcorrections

Multiple corrections to the docs
Merge pull request #917 from ElDeveloper/issue_779

Fixes Issue 779
Change all_tests.py to use get_qiime_scripts_dir()
Merge branch 'master' of github.com:qiime/qiime into update_blast_db
Fixing blast_db option bug
Update denoise_wrapper.py

Sorry for editing so late. I am pretty much noobish in this github-game :-). I just tried this code on some samples and it worked well. Hopefully it workes for you, too. Have a nice weekend all together.
Merge pull request #930 from ElDeveloper/issue_881

Retrieve qiime_scripts_dir on the fly
Merge pull request #925 from josenavas/update_blast_db

Update the blast_db option type across all QIIME scripts
Merge branch 'master' of github.com:josenavas/qiime into count_seqs