Source 2/Docs/Porting Legacy Content/Models
Source 2 has a built-in system for taking old .mdl files from Source 1 and converting them to Source 2. It's not a perfect system and 9 times out of 10, it will not compile, but it can be great if you are porting content en masse from Source 1 to Source 2.
Prerequisites
This system is very picky as to what kind of .mdl formats are imported. Currently, Source Filmmaker so far has been the most successful place to port models from, which can be beneficial as the SFM already ships with content from a ton of games. However, Half-Life 2 and Left 4 Dead 2, among others, have all been tested and are incompatible, but luckily, Valve has already ported a lot of content from those games.
Creating the .vmdl File
To convert the .mdl file, you must first create a structure for your content to live in. Let's say I'm converting a model from Half-Life 2, lets say "models/humans/group01/male_07.mdl" for use in Half-Life: Alyx. To do this, you will need to have the tools installed and a content folder for the mod you're attempting to compile for. In this case, I have a mod called hl2 which has a corresponding folder in my content and game folders inside of "steamapps/content/Half-Life Alyx".
Next, you'll want to drop your .mdl and it's corresponding files into the same file structure it had in Source 1. So for instance, my male_07 model files will now be in "Half-Life Alyx/content/hl2/models/humans/group01/male_07.mdl".
Finally, you'll want to create a new .vmdl file. Open it in your favorite text editor and add the following code to it. Close the file and then open the Source 2 Tools.
<!-- kv3 encoding:text:version{e21c7f3c-8a33-41c5-9977-a76d3a32aa0d} format:generic:version{7412167c-06e9-4698-aff2-e63eb59037e7} -->
{
m_sMDLFilename = "models/humans/group01/male_07.mdl"
}
Once done, you can now open your .vmdl file and it will automatically compile itself to a .vmdl_c file!
The only thing left to do is to create material files which should have the same names and file structures as the Source 1 .vmt files. So for instance, I'd want to create a citizen_sheet.vmat file in the following file structure: materials/models/humans/male/group01/citizen_sheet.vmat

Half-Life: Alyx and ModelDoc
Half-Life Alyx introduced a new model editor called ModelDoc. ModelDoc grants us a much wider variety of what we can do with our models, and allows access to special tools not available in the old Model Editor.
With ModelDoc, you can import an old .vmdl file by clicking File->Import->Import and Convert old .VMDL. When you do this, the model will actually process out all of it's sources, and it will spit out some FBX files for you to mess about with. This is ideal if you want to make modifications to help facilitate your model's transition to Source 2. Currently there's not a known way to batch process all of the .VMDL files in the game, but you can utilize this tool to fix problems with the importer.
Other Notes/Broken Things
The biggest problem this auto-conversion tool has is that flexes are non-functional. Some have their flexes vertex data completely destroyed (such as HWM models from SFM,) some just have a mix of working/non-functioning flexes.
The other problem is the lack of support for certain Source 1 Engine branches, so importing models that haven't already been converted for Source Filmmaker can be quite difficult.