R package installation now cd's to valid directory

Fixes #27.
Merge pull request #33 from jrrideout/r-package-fix

R package installation now cd's to valid directory first.
Add sqlite3 and libsqlite3-dev to README.md
Merge pull request #41 from jrrideout/sqlite-readme

Add sqlite3 and libsqlite3-dev to README.md
added autoconf-make-install-options.
Forgot to clear out the make install options if none are provided.  Added that!
Merge pull request #43 from samfway/make_install_opt

Add autoconf-make-install-options to qiime-deploy (autoconf)
Ignore dangling symlinks in recursive copy

This is necessary to fix an issue we're having with ea-utils (it ships with broken symlinks). Python 3 has a flag to ignore dangling symlinks, but this will have to do for now...