add user option re: allowing path/sig loading failures?

[bluegenes]

For most functions, we allow skipped files (no compatible signatures) and failed files (can't load signature). This makes sense because search results are pretty independent and often accurate even if we miss a few files.

For the index command, I disabled this because we usually want to make sure we have all intended files within the index before running this long command.

With refactoring in #197, I standardized this into an option passed into load_collection. If we want, we could all this to be user-modifiable, e.g. --force option or similar.