MRG: add --output-all-comparisons to manysearch, multisearch, and pairwise

[ctb]

This PR adds -A/--output-all-comparisons to manysearch, multisearch, and pairwise. Updates documentation, adds tests, etc.

A few notes:

• -t/--threshold is ignored when -A is provided.
• manysearch against RocksDB will only output comparisons with some overlap; this is documented.

This PR also:

• adds a note about (lack of) semantic versioning, ref Inconsistent column order output from manysearch #539;
• advises using column names to parse CSV files, ref Inconsistent column order output from manysearch #539;
• removes many of the old version comments ("as of v0.9.whatever, ...") from the documentation;
• checks for directories as input and fails appropriately, per cannot pass directory to multisearch or pairwise #533

Fixes #542
Fixes #539
Fixes #533

TODO:

• add tests

[ctb]

Ready for review & merge @bluegenes

[bluegenes]

lgtm