work around for build_ext config #352

Distribution.reinitialize_command implies that you get the same command
that get_command_obj() but fails to set options that were supplied in
config files or on the command line like Distribution.get_command_obj()
does.

This includes a monkeypatch to fix this issue.
Merge pull request #353 from ged-lab/fix/build_ext-cfg-workaround

work around for build_ext config #352
set fill_id to zero at initialization; Coverity CID 1054789 redux
docs: fork/tag policy, formatting fixes
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/
Merge pull request #322 from ged-lab/extend-docs

docs: fork/tag policy, formatting fixes
demote nose & sphinx to extra dependencies.

Auto-install Python developer tools as needed
Merge pull request #356 from ged-lab/cov-1054789

set IParser::ParserState::ParserState:fill_id to zero at initialization
Merge pull request #351 from ged-lab/feature/relax-dependencies

demote nose & sphinx to extra dependencies.
Merge pull request #357 from ged-lab/fileIOapi

new khmer/file module
don't implicitly downcast tagset_size()

Changes fileformat version for saved tagsets
formatting only; astyle -A10 lib/counting.{cc,hh}
more downcast removal; scope reduction; prefix oper
force 64bit-only builds on OSX
FORMATTING ONLY: astyle -A10
two more downcasts
Merge pull request #339 from ged-lab/fix/nodowncast2

Fix/nodowncast2
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'
mention unification behind @camillescott's khmer_args
make clean is now failproof