Skip based on mtime, not folder

I have one piece of software that manages ingestion of my library and I rely on Beets for proper tagging and naming. I'm having Beets hardlink the files to its own view of the library which works great, but when I change an album it won't pick up the changes because it's skipping the directory. It would be great if instead it could scan and skip importing based on a file's mtime.

Right now I have to work around it by manually re-importing the album directory with `--flat` which works but is very tedious and makes it hard to automate.

Start by tracing the import path and the existing --flat handling to find where directories are skipped. Determine how file modification times should affect scanning, then verify that changed files in an otherwise skipped album are imported without requiring manual re-import; the issue does not name specific files or tests.

Written by the indexing model from the issue text.