document that files in pathlists are relative to the cwd, not to the pathlist location.

[ctb]

currently, the file list returned by load_file_list_of_signatures is assumed to be relative to current working directory; an equally natural behavior would be to load relative paths based on the dirpath of the text file containing the file list.

whatever we decide, the behavior should be documented.

[ctb]

I'm pretty sure this should be relative to cwd, so as to avoid surprises. So this turns into a "make sure documentation reflects this behavior" issue.

[ctb]

it's, uh, interesting to note that we don't actually document pathlists at all anywhere? We refer to --from-file and --query-from-file but not pathlists:

Passing in lists of files¶

Most sourmash commands will also take a --from-file or --query-from-file, which will take the location of a text file containing a list of file paths. This can be useful for situations where you want to specify thousands of queries, or a subset of signatures produced by some other command.

I wonder if we should consider removing pathlist support altogether? I like the explicit nature of --query-from-file and --from-file, and standalone manifests are better for the other pathlist use cases.