demote nose & sphinx to extra dependencies.

Auto-install Python developer tools as needed
new khmer/file module

check_file_status(file_path), check_space(in_files),
check_space_for_hashtable(hash_size), check_valid_file_exists(in_files)

Squash support added & import and usage of file have been updated in all scripts under
scripts/
switch to autoprogram for all scripts

synchronize tests
remove out-dated files
Install sphinx-contrib.autoprogram when needed
add PDF generation to Makefile, doc env vars
remove references to the word 'hash'