Add AGP file export functionality for finished paths

[fedarko]

This has been on the docket for a while. Gonna take care of it soon.

See the AGP specification for details. I guess we'd export node labels for GML input files and node IDs for other input files.

The main thing I'm unsure about is whether or not to prefix node IDs with anything (e.g. NODE_-5 instead of just -5). Will look around a bit to find out.

[fedarko]

An oversight I realized -- since collapsed node groups don't have "label" or "length" data, exporting AGP paths containing collapsed node groups will cause problems (undefined segments in the data, for one).

Fixes for this:

• Even if the input filetype is GML, if the current node is a collapsed node group then just export its ID (instead of trying to export its "label"). I think that's probably the best practice here. (When looking at generated AGP files, it should be simple to determine if the first two characters of the node ID match something like /[BFCY]\d/, and if so we know that the given node is a collapsed node group of the corresponding type.)
• The notion of "length" in the context of a scaffold in an AGP file is a bit odd for collapsed node groups where paths of variable length exist (which is the case for pretty much all node groups except for chains and perfectly-"balanced" bubbles). It's probably ok to just assign each collapsed node group (in standard mode, at least) a length attribute which'll be the sum of all its child contig lengths, and to use this length attribute when creating AGP files.

[fedarko]

wait didn't mean to do that

[fedarko]

forgot to mention it in the commit message, but this has been closed by 4fdc120.