I have an answer for my own question, somewhat:
Meld has two modes:
- VC (Version Control): Meld compares against the VC image of the directory, and ignores the
File Filters option
- Non-VC mode: the filters kick in
This makes somewhat sense, a way.
I use meteor.js which has a .meteor folder for project meta data. In it there are pulled packages, their src and other meta. Many files/folder, in short. The .meteor folder is listed in the .gitignore file, so git excludes it. Meld on the other hand, revisits it and spends a while scanning its sub folders, which seems to take "forever".
I looked for ways to prevent it. One direction was to use the File Filters feature. Another, would be for meld (in VC-mode) skip ignored content.
Meld has a reported issue "Have meld use the .gitignore to limit scanned dir/files", see:
https://bugzilla.gnome.org/show_bug.cgi?id=684400
As of today this issue is fixed (repo head contains it). Looks like it will be in meld ver 3.11.1 and onward. As expected, this fix solves my problem.
As a side note, it might take a while for this fix to get to Deb/Ubuntu, so if you need it, use meld head from: http://meldmerge.org/development.html