misc small fixes

[notestaff]

Misc small fixes. Factoring out parts of #854 not specific to kmer operations.

• added gitignore for emacs backup files
• added printing of defaults to help msgs. fixed log message that always reported an exception when keeping tmp files, even when there was none. added parse_cmd() and run_cmd() utils to cmd.py .
• added developer docs on adding top-level scripts
• fixed comments; added uncompressed_file_type() to util/file.py; improved preservation of tmp files on request
• added misc utils: as_type, subdict, chk
• reduced code duplication in .travis.yml
• added pytest option to mark tests as slow and run them only when --runslow is specified

[notestaff]

Would it be better to break out these changes into separate PRs? Some are general fixes, some are general utils on which #854 relies.