Restructure deploy directory to be nested

[jairideout]

This request was made by a cluster administrator who has installed QIIME using qiime-deploy, and then created an environment module for QIIME (e.g., module load qiime/1.7.0).

Currently qiime-deploy creates a directory for each dependency, and the directory name includes the package name and version. It would easier to migrate a pure qiime-deploy install into a module-based install if the dependency directories were nested, i.e. <deploy directory>/<package name>/<version>.

[bollig]

+1