MRG: support check --upgrade to upgrade old versions of RocksDB/RevIndex

[ctb]

This PR deals with the ramifications of a format change for RocksDB/RevIndex databases that probably occurred around v0.9.7, in which the 'storage' column was added to RevIndex databases. Prior to that version, RevIndex databases always stored sketches externally; see #390, #416, and sourmash-bio/sourmash#3250.

The addition of the 'storage' column breaks when trying to open old RocksDB/RevIndex databases with more recent versions of the plugin; the error message is: Invalid argument: Column family not found: storage.

This PR:

• updates manysearch and fastmultigather so that a slightly better error message is reported;
• upgrades index with an option --upgrade that will open when searching against a RocksDB, they will automatically upgrade the internal RocksDB format from older versions. This is as simple as opening them in read/write mode instead of read-only mode, which permits sourmash to upgrade the RevIndex;
• adds tests for RocksDB/RevIndex databases created with v0.9.5 and v0.9.13 (with both internal and external storage) so that plugin tests will properly detect database format changes.

An alternative solution would be to always open the database in rw mode so that it just gets upgraded automatically, but it gives me the heeby jeebies to open a database in rw mode unnecessarily...

Fixes #580

TODO

• create issue with error message as doc bait

[bluegenes]

I like the idea of having check update them! Can we output a warning from standard check and then have a flag, --update to go ahead and update?

[ctb]

Ready for review & merge!

[ctb]

I like the idea of having check update them! Can we output a warning from standard check and then have a flag, --update to go ahead and update?

implemented!

[bluegenes]

Lgtm!