Hey Mac! Thanks for the reply. I'm a bit torn here - On the one hand, I'm the newb, and you're the experienced developer and longtime user.
And I wouldn't bet that my interpretation of what constitutes a broken dependencies is accurate and exhaustive - I usually learn about the existence of a bug from Meshed's anouncement that he fixed it ... ?
Otoh, I've stored the vast majority of my stuff in subfolders of /AddonPackages/ - including my homegrown morphpacks that my favorite homegrown custom model heavily depends on - and VaM 1.2.0.10 has not done anything that I, with my limited understanding, would interpret as breaking dependencies. It finds the meta.json of a package stored in a subfolder of AddonPackages. It flags dependencies on vars that I am actually missing (though most of the flags are creator's referencing specific versions of files in their meta.json, rather than just using .latest). I haven't yet caught it flagging packages as missing that do I have.
But as I said, my not noticing anything is ... not really what you'd call proof of very much at all, I'm afraid.
I reallyreally don't mean to question your skill or expertise - but could I maybe impose on you and ask you to make a quick & dirty test whether the issues you were experiencing still persist in 1.2.0.10 (whenever you have a few minutes to spare)? I don't mean bughunting - just plonking a single .var that's referenced in one of your current fav scenes into a subfolder, leave it there for a bit, see what happens?